3QKB | pdb_00003qkb

Crystal structure of a Protein with unknown function which belongs to Pfam DUF74 family (PEPE_0654) from Pediococcus pentosaceus ATCC 25745 at 2.73 A resolution

PDB DOI: https://doi.org/10.2210/pdb3QKB/pdb

Classification: Structural Genomics, Unknown function
Organism(s): Pediococcus pentosaceus ATCC 25745
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-01-31 Released: 2011-02-23
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free:
0.239 (Depositor), 0.227 (DCC)
R-Value Work:
0.202 (Depositor), 0.196 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a Protein with unknown function which belongs to Pfam DUF74 family (PEPE_0654) from Pediococcus pentosaceus ATCC 25745 at 2.73 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 63.43 kDa
Atom Count: 3,653
Modeled Residue Count: 464
Deposited Residue Count: 555
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E	111	Pediococcus pentosaceus ATCC 25745	Mutation(s): 0 Gene Names: PEPE_0654
UniProt
Find proteins for Q03GF5 (Pediococcus pentosaceus (strain ATCC 25745 / CCUG 21536 / LMG 10740 / 183-1w)) Explore Q03GF5 Go to UniProtKB: Q03GF5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03GF5
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, E	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.239 (Depositor), 0.227 (DCC)
R-Value Work: 0.202 (Depositor), 0.196 (DCC)
R-Value Observed: 0.204 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33QKB

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.296	α = 90
b = 67.301	β = 90
c = 85.836	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-02-23

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-02-23
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: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Refinement description, 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.