8C7P

Tagless BtuM in complex with cyanocobalamin

PDB DOI: https://doi.org/10.2210/pdb8C7P/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Thiobacillus denitrificans ATCC 25259
Expression System: Escherichia coli MC1061
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2023-01-16 Released: 2024-01-31
Deposition Author(s): Martinez-Felices, J.M., Slotboom, D.J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.263
R-Value Work: 0.225

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of the Thiobacillus denitrificans cobalamin transporter BtuM in complex with cyanocobalamin

Martinez-Felices, J.M., Slotboom, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 23.13 kDa
Atom Count: 1,474
Modelled Residue Count: 179
Deposited Residue Count: 199
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalamin ABC transporter	A	199	Thiobacillus denitrificans ATCC 25259	Mutation(s): 0 Gene Names: Tbd_2719 Membrane Entity: Yes
UniProt
Find proteins for Q3SFD8 (Thiobacillus denitrificans (strain ATCC 25259)) Explore Q3SFD8 Go to UniProtKB: Q3SFD8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3SFD8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.263
R-Value Work: 0.225
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.318	α = 90
b = 91.318	β = 90
c = 77.391	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Coot	model building
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-31

Deposition Author(s):

Martinez-Felices, J.M.

Funding Organization	Location	Grant Number
Other government	Netherlands	--

Revision History (Full details and data files)

Version 1.0: 2024-01-31
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.