2I9X | pdb_00002i9x

Structural Genomics, the crystal structure of SpoVG conserved domain from Staphylococcus epidermidis ATCC 12228

• PDB DOI: https://doi.org/10.2210/pdb2I9X/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Staphylococcus epidermidis ATCC 12228
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-09-06 Released: 2006-10-03 
• Deposition Author(s): Tan, K., Maltseva, N., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

The crystal structure of SpoVG from Staphylococcus epidermidis ATCC 12228

Tan, K., Maltseva, N., Bargassa, M., 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)

Macromolecule Content 

• Total Structure Weight: 20.5 kDa 
• Atom Count: 1,529 
• Modeled Residue Count: 171 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative septation protein spoVG	A, B	87	Staphylococcus epidermidis ATCC 12228	Mutation(s): 5  Gene Names: spoVG, SE_2285
UniProt
Find proteins for Q8CML1 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore Q8CML1  Go to UniProtKB:  Q8CML1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.55	α = 90
b = 64.55	β = 90
c = 97.711	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-03 
Deposition Author(s): Tan, K., Maltseva, N., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-10-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary