4M7O | pdb_00004m7o

The crystal structure of a possible an iron-binding (periplasmic solute-binding) protein from Staphylococcus epidermidis ATCC 12228.

• PDB DOI: https://doi.org/10.2210/pdb4M7O/pdb

• Classification: Iron binding protein
• Organism(s): Staphylococcus epidermidis ATCC 12228
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-12 Released: 2013-08-28 
• Deposition Author(s): Tan, K., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.227 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

The crystal structure of a possible an iron-binding (periplasmic solute-binding) protein from Staphylococcus epidermidis ATCC 12228.

Tan, K., Li, H., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 31.74 kDa 
• Atom Count: 2,092 
• Modeled Residue Count: 258 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-binding protein	A	278	Staphylococcus epidermidis ATCC 12228	Mutation(s): 0  Gene Names: SE_0383
UniProt
Find proteins for A0A0H2VHB1 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore A0A0H2VHB1  Go to UniProtKB:  A0A0H2VHB1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.227 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.052	α = 90
b = 48.173	β = 102.74
c = 44.916	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Tan, K., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary