3GWY | pdb_00003gwy

Crystal structure of putative CTP pyrophosphohydrolase from Bacteroides fragilis

PDB DOI: https://doi.org/10.2210/pdb3GWY/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-04-01 Released: 2009-04-14
Deposition Author(s): Patskovsky, Y., Romero, R., Gilmore, M., Do, J., 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: 2.00 Å
R-Value Free:
0.271 (Depositor), 0.275 (DCC)
R-Value Work:
0.216 (Depositor), 0.217 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3GWY

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

Literature

Crystal Structure of Ctp Pyrophosphohydrolase from Bacteroides fragilis

Patskovsky, Y., Romero, R., Gilmore, M., Do, J., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 32.71 kDa
Atom Count: 2,204
Modeled Residue Count: 254
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative CTP pyrophosphohydrolase	A, B	140	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF2916 EC: 3.6.1.55
UniProt
Find proteins for Q5LBB1 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LBB1 Go to UniProtKB: Q5LBB1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LBB1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.271 (Depositor), 0.275 (DCC)
R-Value Work: 0.216 (Depositor), 0.217 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.138	α = 90
b = 62.275	β = 90
c = 59.777	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-04-14

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2018-11-21
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Structure summary
Version 1.5: 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.