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)

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 3O6P

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of peptide ABC transporter, peptide-binding protein

Chang, C., Bigelow, L., Bearden, J., Joachimiak, A.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q837D6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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Entry History

Deposition Data

Released Date: 2010-09-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.