6FXG | pdb_00006fxg

Crystal structure of substrate binding domain 1 (SBD1) OF ABC transporter GLNPQ in complex with Asparagine

PDB DOI: https://doi.org/10.2210/pdb6FXG/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Lactococcus lactis subsp. lactis
Expression System: Lactococcus lactis
Mutation(s): No

Deposited: 2018-03-09 Released: 2019-03-20
Deposition Author(s): Guskov, A., Schuurman-Wolters, G.K., Poolman, B.
Funding Organization(s): ERC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.170 (Depositor), 0.180 (DCC)
R-Value Work:
0.136 (Depositor), 0.150 (DCC)
R-Value Observed:
0.138 (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 1 (SBD1) OF ABC transporter GLNPQ in complex with Asparagine

Schuurman-Wolters, G.K., Guskov, A., Poolman, B.

To be published.

Macromolecule Content

Total Structure Weight: 74.52 kDa
Atom Count: 6,254
Modeled Residue Count: 675
Deposited Residue Count: 681
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 membrane protein PAAT family	A, B, C	227	Lactococcus lactis subsp. lactis	Mutation(s): 0 Gene Names: LL275_1813
UniProt
Find proteins for Q9CES5 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CES5 Go to UniProtKB: Q9CES5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CES5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASN Query on ASN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	ASPARAGINE C₄ H₈ N₂ O₃ DCXYFEDJOCDNAF-REOHCLBHSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.170 (Depositor), 0.180 (DCC)
R-Value Work: 0.136 (Depositor), 0.150 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.87	α = 90
b = 74.27	β = 90.55
c = 110.24	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Schuurman-Wolters, G.K.

Funding Organization	Location	Grant Number
ERC	Netherlands	ABCvolume, #670578

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2024-01-17
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.