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SSRL Headlines Vol. 6, No. 11  June, 2006


Contents of this Issue:

  1. Science Highlight — Chemists Discover how Nature Makes Medicine
  2. Science Highlight — Protecting against DNA Invasion
  3. SPEAR3 Fast Orbit Feedback Milestone Achieved in June
  4. Register for SSRL Summer Workshops in the Structural Biology Sciences
  5. Call for Nominations for Klein, Spicer and Lytle Awards
  6. Stanford Board of Trustees Committee Visits SLAC
  7. Secretary of Energy Bodman Speaks to DOE Employees
  8. Summer Public Science Lectures at SLAC and Stanford University
  9. More SSRL News for a Wider Audience
  10. Macromolecular Crystallography Proposals due July 1
  11. Photon Science Job Opportunities

1.  Science Highlight — Chemists Discover how Nature Makes Medicine
      (contact: C.L. Drennan,

After years of wondering how organisms managed to create medically valuable natural products, like antibiotics and anti-fungal agents, chemists have discovered the surprisingly simple secret by shining x-ray light on the problem. MIT and Harvard researchers used crystallography beam lines at the Stanford Synchrotron Radiation Laboratory and the Advanced Light Source in Berkeley for their research.

They determined the atomic structure of an iron-dependent halogenase, the enzyme SyrB2, from the plant pathogen Pseudomonas syringae. This enzyme catalyzes the chlorination of threonine during biosynthesis of the anti-fungal agent syringomycin, a natural-product antibiotic. This provides one example of how an enzyme can coax a reaction to generate medically valuable halogenated natural products. The products include antibiotics, anti-tumor agents and fungicides, and they are challenging to synthesize in a laboratory. The crystallography study revealed in this case how the specific structure at the iron-containing active site of the enzyme (the site responsible for the chemical reaction) provides information that can help in understanding how the chemical process takes place.

Crystal structure of the non-heme iron halogenase SyrB2.
The structure revealed a novel coordination for iron that contains a chloride ion together with two histidine amino acids, a deviation from the way an iron atom is normally held in an enzyme's active site of this kind in that it does not contain a carboxylate-containing amino acid. The position of the surrounding amino acids indicate that the structure has more room at the active site, enough space for the chloride to enter and bind to the iron as part of the chemical reaction.

"Now that we have the enzyme's structure and figured out how it works, it makes sense. But it's not what we would have predicted," said Catherine Drennan of MIT. "Things are usually not this simple, but there's an elegant beauty in this simplicity," one that might help chemistry labs gain the enzyme's capabilities.

To learn more about this research see the full technical highlight at:

2.  Science Highlight — Protecting against DNA Invasion
      (contact: G. Balendiran,

Dimer of C.BclI structure.
X-ray studies conducted at SSRL have shed light on a sword-and-shield type of defense used by bacteria to protect themselves from viral attacks. This new knowledge could prove significant to medical research on human cancers caused by a similar defense mechanism gone awry.

Researchers from the City of Hope cancer research and treatment center in Duarte, California, determined the crystal structure of the protein that controls this defense system in bacteria called Bacillus caldolyticus. Unless stopped, viral DNA slips into bacterial DNA, where it gets copied many times over, and then destroys its host. To protect bacterial cells, the control protein ensures the proper ratio between two enzymes, the "swords" and the "shields." The sword enzyme slashes invading viral DNA into useless pieces. The shield enzyme adds a protective layer to bacterial DNA, so the sword will not cut its master. Too few shields lead to bacterial cell death, and too many shields protect the viral DNA as well.

The crystal structure of the control protein uncovers the presence of a helix-turn-helix (HTH) motif which has the potential to bend B-DNA. The structural study also revealed amino acid residues that are most likely involved in the DNA interaction. The proposed model suggests that the protein adjusts the levels of the defense enzymes (swords and shields) by sliding along the bacterial DNA, bending and changing its shape to turn on or off the respective genes.

To learn more about this research see the full technical highlight at:

3.   SPEAR3 Fast Orbit Feedback Milestone Achieved in June
      (contact: R. Hettel,

On June 14, the SSRL Accelerator Systems Department commissioned an improved system designed to stabilize electron beam orbit in a frequency bandwidth approaching 100 Hz. The Fast Orbit Feedback System replaces the slower version, which corrects the orbit every few seconds, and that has been in use since SPEAR3 became operational. The new system acquires electron orbit and photon beam position data and updates the orbit correction magnets at a 4 kHz rate using a high speed distributed processing network. The system is effective in suppressing beam motion up to a few 10s of Hz caused by magnet support girder vibration, traffic near the SPEAR3 complex, and, most notably, disturbances arising from user-controlled insertion device changes. Work is continuing to improve and optimize fast orbit feedback performance.

4.  Register for SSRL Summer Workshops in the Structural Biology Sciences

July 28-30, 2006: Workshop on Small-Angle X-ray Scattering and Diffraction Studies in Structural Biology. Organized by Hiro Tsuruta, Thomas Weiss and Marc Niebuhr (SSRL), this workshop will provide hands-on training on experimental techniques, software tutorial sessions primarily for solution x-ray scattering studies, and talks on recent applications. Several shifts of beam time have been allocated for short periods of data collection by workshop participants. Register at:

August 4, 2006: SSRL Crystallography Remote Access Workshop. There are still a few slots remaining for this workshop which will be held at the Hauptman-Woodward Medical Research Institute in Buffalo, NY on August 4. Organizers Aina Cohen and Clyde Smith (SSRL), and Edward Snell (HWI) are planning an agenda that will start with lectures and a live demonstration of remote access data collection followed by two hands-on training sessions. Attendees will learn about the beam line and software developments and how to successfully complete all stages of a remote access experiment. For more information and to register see:

5.  Call for Nominations for Klein, Spicer and Lytle Awards

Please take a few moments to consider nominating your colleagues for one or more of the following awards which will be presented at the 33rd Annual SSRL Users' Meeting, October 12-13, 2006:

Earlier this year, the SSRL Users' Organization Executive Committee (SSRLUOEC) established a Scientific Development Award to honor Melvin P. Klein (1921-2000), a pioneer at the forefront of accomplishments in NMR, EPR, and x-ray absorption spectroscopy who was dedicated to the pursuit of the structure of the Mn complex characterized by the interplay of these methods. The Melvin P. Klein Scientific Development Award will be given to an undergraduate or graduate student to disseminate scientific results based on work performed at SSRL. The award (up to $1,000) will reimburse a student to present their work at a scientific conference during the following year. The recipient will be selected by a user subcommittee based on a nomination package which should include a letter of recommendation from the advisor; an abstract written by the candidate describing the experiment and scientific results (not to exceed 300 words); and information on when and where the work is to be presented. Nominations must be received by August 1. Additional instructions and information on making a donation toward this award are available at:

Submit nominations for the William E. Spicer Young Investigator Award by August 1. The Spicer Award was established in 2004 to honor Bill Spicer (1929-2004), one of the original founders of the Stanford Synchrotron Radiation Project. This award recognizes important technical or scientific accomplishments that benefited from, or are beneficial to, the SSRL. The award is open to senior graduate students and PhDs within seven years of entry into their professional scientific field. The award consists of a certificate and $1,000 as well as waived registration and travel support to make a presentation at SSRL33 on October 12-13. Nominations in the form of a letter or email summarizing the technical or scientific contributions of the candidate must be sent to Cathy Knotts ( before August 1. Nominations should include the candidate's CV and publications; supporting letters are also encouraged.

Submit nominations for 2006 Farrel W. Lytle Award by August 15. The Lytle Award was established by the SSRLUOEC to promote important technical or scientific accomplishments in synchrotron radiation-based science and to foster collaboration and efficient use of beam time among users and staff at SSRL. The award consists of a certificate and $1,000. All SSRL users and staff are eligible for this award. The recipient will be selected by the SSRLUOEC, and the award will be presented at the SSRL33 awards dinner on Thursday, October 12, 2006. Nominations summarizing the individual's contributions and why they should be recognized through this award must be sent before the August 15 deadline to Cathy Knotts (

6.   Stanford Board of Trustees Committee Visits SLAC

Board of Trustees
Committee at BL11-1
Tour Stop at BL 11-1
The Committee on Academic Policy, Planning and Management of the Stanford Board of Trustees visited SLAC on Wednesday, June 14. After hearing an overview of the SLAC scientific program by SLAC Director Jonathan Dorfan and remarks by KIPAC Director Roger Blandford on the Particle Astrophysics and Cosmology Program, they toured the site, including brief stops at three SSRL beam lines where they heard from Keith Hodgson, Jennifer Leisch and Gordon Brown about the role of synchrotron-related science in pharmaceutical drug discovery, research towards a hydrogen economy and efforts aimed at restoring our polluted environment, respectively.

7.   Secretary of Energy Bodman Speaks to DOE Employees

Secretary Bodman
On Wednesday, June 14, Department of Energy Secretary Samuel Bodman reached out to all 116,000 Department of Energy (DOE) federal and contractor employees via live broadcast to express his appreciation for the work behind a number of remarkable DOE achievements over the past year and to discuss future challenges and opportunities within the organization. Secretary Bodman also stressed the importance of a safe workplace. For a full transcript of his remarks see:

8.   Summer Public Science Lectures at SLAC and Stanford University

the thinker
The Thinker, 1880-1881. Promised gift to the Iris & B. Gerald Cantor Center for Visual Arts at Stanford University
Kavli Institute for Particle Astrophysics and Cosmology (KIPAC) astrophysicist Sarah Church will give a SLAC public lecture, "Whispers of the Big Bang", on Tuesday, June 27, at 7:30 p.m. in the SLAC Panofsky Auditorium.

On Tuesday, August 29, Sean Brennan (SSRL) will give the next lecture in the series on "A Comet on Earth: Results from the Stardust Mission."

Uwe Bergmann (SSRL) will give a talk titled "Archimedes: Ancient Text Revealed with X-ray Vision on Thursday, August 3, as part of a series of outdoor science lectures held this summer at the Stanford Cantor Arts Center. Parking, museum entrance and lectures are free. Visitors can explore the Cantor Center starting at 5 p.m. and then migrate outside to hear scientists talk in lay terms about their research starting at 7 p.m. For the full schedule and directions see:

9.   More SSRL News for a Wider Audience

Several months ago, SLAC began distributing an electronic daily newsletter, SLAC Today. With additional communications staff, we are able to feature more articles about SSRL activities written for the general public in SLAC Today as well as in this monthly newsletter. See the following for some of the more recent articles. To subscribe to SLAC Today, visit

7-2 mono
Beam Line 7-2 monochromator.
Cool Running for SSRL. As SSRL prepares to turn up the juice to 500 mA, engineers are busily upgrading components to handle the increased power. Key among these components are the monochromators, devices that allow researchers to fine-tune the x-ray beams to the needs of the experiment. Read more at

Why the Aluminum Foil? Perhaps you've noticed that physicists seem to love aluminum foil. Give them a high-precision, expensive vacuum chamber and what do they do with it? Wrap the whole thing like leftovers. The real story, of course, is more complicated than an arbitrary love for shiny things. Foil is used for many things in the lab, and it turns out that when it comes to vacuum chambers, aluminum foil is crucial to developing an ultra-high vacuum. Read more at

10.   Macromolecular Crystallography Proposals due July 1
      (contact: L. Dunn,

July 1, 2006 is the next deadline for submitting macromolecular crystallography proposals. Proposals submitted in July will be eligible for beam time beginning in November 2006. For more information see Proposal Submittal and Scheduling Procedures for Macromolecular Beam Lines at SSRL.

11.   Photon Science Job Opportunities

A number of positions are currently available at the LCLS, LUSI and SSRL. Please refer to the Photon Science Job Openings page for more information about these job opportunities.


SSRL Headlines is published electronically monthly to inform SSRL users, sponsors and other interested people about happenings at SSRL. SSRL is a national synchrotron user facility operated by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. Additional support for the structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH Institute for General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 28 JUN 2006
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