3MXU | pdb_00003mxu

Crystal structure of glycine cleavage system protein H from Bartonella henselae

• PDB DOI: https://doi.org/10.2210/pdb3MXU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bartonella henselae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-07 Released: 2010-05-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.196 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glycine cleavage system protein H from Bartonella henselae

Edwards, T.E., Gardberg, A.S., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.15 kDa 
• Atom Count: 1,223 
• Modeled Residue Count: 134 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine cleavage system H protein	A	143	Bartonella henselae	Mutation(s): 0  Gene Names: gcvH, BH12830
UniProt
Find proteins for Q6G2F0 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1)) Explore Q6G2F0  Go to UniProtKB:  Q6G2F0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.196 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33MXU

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.91	α = 90
b = 98.91	β = 90
c = 131.54	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description