4ZEF | pdb_00004zef

Crystal structure of substrate binding domain 2 (SBD2) OF ABC transporter GLNPQ from Enterococcus faecalis

PDB DOI: https://doi.org/10.2210/pdb4ZEF/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Enterococcus faecalis V583
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-20 Released: 2016-06-29
Deposition Author(s): Fulyani, F., Guskov, A., Poolman, B.
Funding Organization(s): NWO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.158 (Depositor), 0.170 (DCC)
R-Value Work:
0.129 (Depositor), 0.140 (DCC)
R-Value Observed:
0.130 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of substrate binding domain 2 (SBD2) OF ABC transporter GLNPQ from Enterococcus faecalis

Fulyani, F., Guskov, A., Poolman, B.

To be published.

Macromolecule Content

Total Structure Weight: 28.26 kDa
Atom Count: 2,326
Modeled Residue Count: 239
Deposited Residue Count: 251
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC transporter amino acid-binding/permease	A	251	Enterococcus faecalis V583	Mutation(s): 0 Gene Names: EF_0761, I574_01170, OO5_02671
UniProt
Find proteins for Q837S0 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837S0 Go to UniProtKB: Q837S0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q837S0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLN Query on GLN 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]	GLUTAMINE C₅ H₁₀ N₂ O₃ ZDXPYRJPNDTMRX-VKHMYHEASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.158 (Depositor), 0.170 (DCC)
R-Value Work: 0.129 (Depositor), 0.140 (DCC)
R-Value Observed: 0.130 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.14	α = 90
b = 81.14	β = 90
c = 102.38	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Funding Organization	Location	Grant Number
NWO	Netherlands	--

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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.