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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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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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

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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.