4QGR | pdb_00004qgr

Crystal structure of a DegT DnrJ EryC1 StrS aminotransferase from Brucella abortus

• PDB DOI: https://doi.org/10.2210/pdb4QGR/pdb

• Classification: TRANSFERASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-23 Released: 2014-06-18 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.185 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a DegT DnrJ EryC1 StrS family protein from Bartonella abortus

Edwards, T.E., Fairman, J.W., Letesson, J.J., Seattle Structural Genomics Center for Infectious Disease

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 83.84 kDa 
• Atom Count: 6,459 
• Modeled Residue Count: 749 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DegT/DnrJ/EryC1/StrS aminotransferase	A, B	382	Brucella abortus 2308	Mutation(s): 0  Gene Names: BAB1_1616
UniProt
Find proteins for Q2YRB9 (Brucella abortus (strain 2308)) Explore Q2YRB9  Go to UniProtKB:  Q2YRB9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
ACT	D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.185 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34QGR

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.69	α = 90
b = 92.06	β = 96.82
c = 86.41	γ = 90

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: 2014-06-18 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description