6EYL

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
R-Value Work: 0.161
R-Value Observed: 0.163

Starting Model: experimental
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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
Modelled Residue Count: 555
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.192
R-Value Work: 0.161
R-Value Observed: 0.163
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.