2GU3

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 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.214 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• 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

Entry History 

Deposition Data

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

Revision History  

• 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