4HBR | pdb_00004hbr

Crystal structure of a putative periplasmic proteins (BACEGG_01429) from Bacteroides eggerthii DSM 20697 at 2.40 A resolution

PDB DOI: https://doi.org/10.2210/pdb4HBR/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Bacteroides eggerthii DSM 20697
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-28 Released: 2013-02-27
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.213 (Depositor), 0.230 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a putative periplasmic proteins (BACEGG_01429) from Bacteroides eggerthii DSM 20697 at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 64.06 kDa
Atom Count: 4,802
Modeled Residue Count: 559
Deposited Residue Count: 560
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 periplasmic protein	A, B, C, D	140	Bacteroides eggerthii DSM 20697	Mutation(s): 0 Gene Names: BACEGG_01429, ZP_03458652.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.213 (Depositor), 0.230 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.197 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34HBR

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.638	α = 90
b = 117.638	β = 90
c = 150.125	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-02-27

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-02-27
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-02-01
Changes: Database references, Derived calculations
Version 1.3: 2024-11-27
Changes: Data collection, Structure summary

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.