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)

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), 0.166 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein Atu0492	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7D1C9
Sequence Annotations Expand
Reference Sequence

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), 0.166 (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

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Entry History

Deposition Data

Released Date: 2006-05-09

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.