2GU3 | pdb_00002gu3

YpmB protein from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb2GU3/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-04-28 Released: 2006-05-30
Deposition Author(s): Osipiuk, J., Maltseva, N., Dementieva, I., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.214 (Depositor), 0.184 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2GU3

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

Literature

X-ray crystal structure of YpmB protein from Bacillus subtilis.

Osipiuk, J., Maltseva, N., Dementieva, I., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 15.11 kDa
Atom Count: 1,165
Modeled Residue Count: 128
Deposited Residue Count: 136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YpmB protein	A	136	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: ypmB, BSU22380
UniProt
Find proteins for P54396 (Bacillus subtilis (strain 168)) Explore P54396 Go to UniProtKB: P54396
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54396
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.214 (Depositor), 0.184 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.2	α = 90
b = 52.415	β = 90
c = 55.079	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
SCALEPACK	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-05-30

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-05-30
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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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.