2R9Q | pdb_00002r9q

Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium tumefaciens

PDB DOI: https://doi.org/10.2210/pdb2R9Q/pdb

Classification: HYDROLASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-09-13 Released: 2007-10-02
Deposition Author(s): Zhang, R., Dong, A., Xu, X., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.269 (Depositor), 0.293 (DCC)
R-Value Work:
0.189 (Depositor), 0.218 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2R9Q

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium tumefaciens.

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

To be published.

Macromolecule Content

Total Structure Weight: 163.82 kDa
Atom Count: 10,768
Modeled Residue Count: 1,346
Deposited Residue Count: 1,496
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-deoxycytidine 5'-triphosphate deaminase	A, B, C, D	370	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: dcd, AGR_C_764, Atu0434
UniProt
Find proteins for A9CKA1 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CKA1 Go to UniProtKB: A9CKA1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9CKA1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic peptide 1	E [auth X]	7	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic peptide 2	F [auth Y]	9	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.269 (Depositor), 0.293 (DCC)
R-Value Work: 0.189 (Depositor), 0.218 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.693	α = 90
b = 129.042	β = 108.75
c = 85.559	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-02

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-10-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-02-21
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.