3EVY

Crystal structure of a fragment of a putative type I restriction enzyme R protein from Bacteroides fragilis

PDB DOI: https://doi.org/10.2210/pdb3EVY/pdb

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

Deposited: 2008-10-13 Released: 2008-10-21
Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Miller, S., Sampathkumar, P., 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: 1.95 Å
R-Value Free: 0.274
R-Value Work: 0.229
R-Value Observed: 0.231

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a fragment of a putative type I restriction enzyme R protein from Bacteroides fragilis

Bonanno, J.B., Gilmore, M., Bain, K.T., Miller, S., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 55.7 kDa
Atom Count: 1,511
Modelled Residue Count: 167
Deposited Residue Count: 478
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative type I restriction enzyme R protein	A, B	239	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF1836, hsdR
UniProt
Find proteins for Q5LEB7 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5LEB7 Go to UniProtKB: Q5LEB7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LEB7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.274
R-Value Work: 0.229
R-Value Observed: 0.231
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.834	α = 90
b = 56.47	β = 90
c = 75.857	γ = 90

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-10-21

Deposition Author(s):

Sampathkumar, P.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-10-21
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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.