2GMY | pdb_00002gmy

Crystal Structure of a Protein of Unknown Function ATU0492 from Agrobacterium tumefaciens, Putative Antioxidant Defence Protein AhpD

• PDB DOI: https://doi.org/10.2210/pdb2GMY/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-04-07 Released: 2006-05-09 
• Deposition Author(s): Zhang, R., Xu, X., Gu, J., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

The crystal structure of a hypothetical protein Atu0492 from Agrobacterium tumefaciens

Zhang, R., Xu, X., Gu, J., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 102.81 kDa 
• Atom Count: 7,730 
• Modelled Residue Count: 876 
• Deposited Residue Count: 918 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein Atu0492	A, B, C, D, E, F	153	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: GI:17934405
UniProt
Find proteins for Q7D1C9 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D1C9  Go to UniProtKB:  Q7D1C9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.009	α = 90
b = 75.009	β = 90
c = 148.755	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-09 
Deposition Author(s): Zhang, R., Xu, X., Gu, J., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-05-09
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references