2HRZ | pdb_00002hrz

The crystal structure of the nucleoside-diphosphate-sugar epimerase from Agrobacterium tumefaciens

PDB DOI: https://doi.org/10.2210/pdb2HRZ/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-07-20 Released: 2006-08-22
Deposition Author(s): Zhang, R., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.225 (Depositor), 0.223 (DCC)
R-Value Work:
0.185 (Depositor), 0.183 (DCC)
R-Value Observed:
0.186 (Depositor)

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

Literature

The crystal structure of the nucleoside-diphosphate-sugar epimerase from Agrobacterium tumefaciens

Zhang, R., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 37.56 kDa
Atom Count: 2,937
Modeled Residue Count: 342
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside-diphosphate-sugar epimerase	A	342	Agrobacterium fabrum str. C58	Mutation(s): 7 Gene Names: AGR_C_4963, Atu2738
UniProt
Find proteins for A9CHF5 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CHF5 Go to UniProtKB: A9CHF5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9CHF5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.225 (Depositor), 0.223 (DCC)
R-Value Work: 0.185 (Depositor), 0.183 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.893	α = 90
b = 112.893	β = 90
c = 52.765	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
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: 2006-08-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-08-22
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.