2FPN | pdb_00002fpn

The crystal structure of the ywmB protein from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb2FPN/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2006-01-16 Released: 2006-03-14
Deposition Author(s): Zhang, R., Wu, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.281 (Depositor), 0.278 (DCC)
R-Value Work:
0.242 (Depositor)
R-Value Observed:
0.244 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of the ywmB protein from Bacillus subtilis

Zhang, R., Wu, R., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 25.69 kDa
Atom Count: 1,753
Modeled Residue Count: 205
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ywmB	A	216	Bacillus subtilis	Mutation(s): 8 Gene Names: ywmB
UniProt
Find proteins for O32277 (Bacillus subtilis (strain 168)) Explore O32277 Go to UniProtKB: O32277
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O32277
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.281 (Depositor), 0.278 (DCC)
R-Value Work: 0.242 (Depositor)
R-Value Observed: 0.244 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.79	α = 90
b = 50.856	β = 96.49
c = 81.259	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-03-14

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-03-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.