3S30

Crystal structure of a putative glycoside hydrolase (BVU_0247) from Bacteroides vulgatus ATCC 8482 at 2.46 A resolution

PDB DOI: https://doi.org/10.2210/pdb3S30/pdb

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

Deposited: 2011-05-17 Released: 2011-06-08
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.251
R-Value Work: 0.233
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Crystal structure of a Hypothetical glycoside hydrolase (BVU_0247) from Bacteroides vulgatus ATCC 8482 at 2.46 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 79.17 kDa
Atom Count: 4,145
Modelled Residue Count: 510
Deposited Residue Count: 708
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical glycoside hydrolase	A, B	354	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0 Gene Names: BVU_0247
UniProt
Find proteins for A6KX05 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6KX05 Go to UniProtKB: A6KX05
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6KX05
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.251
R-Value Work: 0.233
R-Value Observed: 0.233
Space Group: P 6₅
Diffraction Data: https://doi.org/10.18430/M33S30

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.745	α = 90
b = 146.745	β = 90
c = 91.51	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2011-11-16
Changes: Structure summary
Version 1.4: 2014-12-24
Changes: Structure summary
Version 1.5: 2017-11-08
Changes: Refinement description
Version 1.6: 2018-01-24
Changes: Database references
Version 1.7: 2023-02-01
Changes: Database references, Derived calculations

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.