3E7P | pdb_00003e7p

CRYSTAL STRUCTURE OF of putative methyltransferase from Bacteroides vulgatus ATCC 8482

PDB DOI: https://doi.org/10.2210/pdb3E7P/pdb

Classification: TRANSFERASE
Organism(s): Phocaeicola vulgatus ATCC 8482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-18 Released: 2008-09-02
Deposition Author(s): Malashkevich, V.N., Toro, R., Meyer, A.J., 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: 1.90 Å
R-Value Free:
0.217 (Depositor), 0.214 (DCC)
R-Value Work:
0.184 (Depositor), 0.183 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

CRYSTAL STRUCTURE OF of putative methyltransferase from Bacteroides vulgatus ATCC 8482

Malashkevich, v.n., Toro, R., meyer, A.J., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 30.78 kDa
Atom Count: 2,245
Modeled Residue Count: 253
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A	270	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0 Gene Names: BVU_3255
UniProt
Find proteins for A6L5C0 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L5C0 Go to UniProtKB: A6L5C0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6L5C0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.217 (Depositor), 0.214 (DCC)
R-Value Work: 0.184 (Depositor), 0.183 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.702	α = 90
b = 103.568	β = 90
c = 132.809	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-09-02

Deposition Author(s):

Malashkevich, V.N.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-09-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Derived calculations, 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.