Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15244.58 
• Atom Count: 1004 
• Residue Count: 142 
• Unique protein chains: 1

3IFT

Crystal structure of glycine cleavage system protein H from Mycobacterium tuberculosis, using X-rays from the Compact Light Source.

• DOI: 10.2210/pdb3IFT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2009-07-25 Released: 2009-08-11 
• Deposition Author(s): Edwards, T.E., Abendroth, J., Staker, B., Mayer, C., Phan, I., Kelley, A., Analau, E., Leibly, D., Rifkin, J., Loewen, R., Ruth, R.D., Stewart, L.J., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.253 
• R-Value Work: 0.181 

Literature

X-ray structure determination of the glycine cleavage system protein H of Mycobacterium tuberculosis using an inverse Compton synchrotron X-ray source.

Abendroth, J., McCormick, M.S., Edwards, T.E., Staker, B., Loewen, R., Gifford, M., Rifkin, J., Mayer, C., Guo, W., Zhang, Y., Myler, P., Kelley, A., Analau, E., Hewitt, S.N., Napuli, A.J., Kuhn, P., Ruth, R.D., Stewart, L.J.

(2010) J.Struct.Funct.Genom. 11: 91-100

• PubMed: 20364333 
• DOI: 10.1007/s10969-010-9087-6
• Primary Citation of Related Structures:  
  3HGB


• PubMed Abstract: 
  

Structural genomics discovery projects require ready access to both X-ray diffraction and NMR spectroscopy which support the collection of experimental data needed to solve large numbers of novel protein structures. The most productive X-ray crystal structure determination laboratories make extensive use of tunable synchrotron X-ray light to solve novel structures by anomalous diffraction methods. This requires that frozen cryo-protected crystals be shipped to large multi acre synchrotron facilities for data collection. In this paper we report on the development and use of the first laboratory-scale synchrotron light source capable of performing many of the state-of-the-art synchrotron applications in X-ray science. This Compact Light Source is a first-in-class device that uses inverse Compton scattering to generate X-rays of sufficient flux, tunable wavelength and beam size to allow high-resolution X-ray diffraction data collection from protein crystals. We report on benchmarking tests of X-ray diffraction data collection with hen egg white lysozyme, and the successful high-resolution X-ray structure determination of the Glycine cleavage system protein H from Mycobacterium tuberculosis using diffraction data collected with the Compact Light Source X-ray beam.

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Organizational Affiliation: 

Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glycine cleavage system H protein	A	142	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Gene Names: gcvH
Find proteins for P9WN55 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WN55

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.253 
• R-Value Work: 0.181 
• Space Group: C 1 2 1
• Diffraction Data DOI: 
  10.18430/M33IFT Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 86.450	α = 90.00
b = 51.010	β = 95.10
c = 32.570	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-25 
• Released Date: 2009-08-11 
• Deposition Author(s): Edwards, T.E., Abendroth, J., Staker, B., Mayer, C., Phan, I., Kelley, A., Analau, E., Leibly, D., Rifkin, J., Loewen, R., Ruth, R.D., Stewart, L.J., Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)

Revision History 

• Version 1.0: 2009-08-11
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2018-04-04
  Type: Data collection