3F13 | pdb_00003f13

Crystal structure of putative nudix hydrolase family member from Chromobacterium violaceum

PDB DOI: https://doi.org/10.2210/pdb3F13/pdb

Classification: HYDROLASE
Organism(s): Chromobacterium violaceum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-10-27 Released: 2008-11-25
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Do, J., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.264 (Depositor), 0.269 (DCC)
R-Value Work:
0.221 (Depositor), 0.229 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3F13

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative nudix hydrolase family member from Chromobacterium violaceum

Bonanno, J.B., Freeman, J., Bain, K.T., Do, J., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 37.03 kDa
Atom Count: 2,432
Modeled Residue Count: 287
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative nudix hydrolase family member	A, B	163	Chromobacterium violaceum	Mutation(s): 0 Gene Names: CV_1928
UniProt
Find proteins for Q7NWQ3 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NWQ3 Go to UniProtKB: Q7NWQ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7NWQ3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.264 (Depositor), 0.269 (DCC)
R-Value Work: 0.221 (Depositor), 0.229 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.95	α = 73.47
b = 43.877	β = 74.06
c = 55.967	γ = 62.66

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Structure summary
Version 1.5: 2023-12-27
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.