6EYL | pdb_00006eyl

Crystal structure of OpuBC in complex with carnitine

PDB DOI: https://doi.org/10.2210/pdb6EYL/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-13 Released: 2018-11-21
Deposition Author(s): Peherstorfer, S., Teichmann, L., Smits, S.H., Sschmitt, L., Bremer, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.161 (Depositor), 0.160 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Reprogramming the substrate specificity of an ABC import system by a single amino acid substitution in its cognate ligand binding protein

Peherstorfer, S., Teichmann, L., Smits, S.H., Schmitt, L., Bremer, E.

To be published.

Macromolecule Content

Total Structure Weight: 69.19 kDa
Atom Count: 5,532
Modeled Residue Count: 555
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Osmotically activated L-carnitine/choline ABC transporter substrate-binding protein OpuCC	A, B	306	Bacillus subtilis	Mutation(s): 0 Gene Names: B4417_3194
UniProt
Find proteins for Q45462 (Bacillus subtilis (strain 168)) Explore Q45462 Go to UniProtKB: Q45462
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q45462
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
152 Query on 152 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	CARNITINE C₇ H₁₆ N O₃ PHIQHXFUZVPYII-ZCFIWIBFSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.161 (Depositor), 0.160 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.71	α = 90
b = 66.61	β = 91.84
c = 126.99	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Peherstorfer, S.

Revision History (Full details and data files)

Version 1.0: 2018-11-21
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.