3O6P | pdb_00003o6p

Crystal structure of peptide ABC transporter, peptide-binding protein

• PDB DOI: https://doi.org/10.2210/pdb3O6P/pdb

• Classification: PROTEIN BINDING
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-07-29 Released: 2010-09-22 
• Deposition Author(s): Chang, C., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Crystal structure of peptide ABC transporter, peptide-binding protein

Chang, C., Bigelow, L., Bearden, J., 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: 25.43 kDa 
• Atom Count: 2,278 
• Modeled Residue Count: 227 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide ABC transporter, peptide-binding protein	A	229	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF_0907
UniProt
Find proteins for Q837D6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837D6  Go to UniProtKB:  Q837D6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 1.65 Å
• R-Value Free:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.733	α = 90
b = 53.653	β = 90
c = 79.498	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
Coot	model building
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Chang, C., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.3: 2024-11-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary