2IA9 | pdb_00002ia9

Structural Genomics, the crystal structure of SpoVG from Bacillus subtilis subsp. subtilis str. 168

• PDB DOI: https://doi.org/10.2210/pdb2IA9/pdb

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


• Deposited: 2006-09-07 Released: 2006-10-17 
• Deposition Author(s): Tan, K., Borovilos, M., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of SpoVG from Bacillus subtilis subsp. subtilis str. 168

Tan, K., Borovilos, M., Abdullah, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.75 kDa 
• Atom Count: 4,499 
• Modeled Residue Count: 548 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative septation protein spoVG	A, B, C, D, E, F	100	Bacillus subtilis	Mutation(s): 3  Gene Names: spoVG, BSU00490
UniProt
Find proteins for P28015 (Bacillus subtilis (strain 168)) Explore P28015  Go to UniProtKB:  P28015

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth A], I [auth A], J [auth A], K [auth A], M [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	G [auth A], L [auth B], N [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.464	α = 90
b = 136.464	β = 90
c = 110.493	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Tan, K., Borovilos, M., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary