8OVV | pdb_00008ovv

Tagless BtuM in complex with hydroxycobalamin

• PDB DOI: https://doi.org/10.2210/pdb8OVV/pdb

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


• Deposited: 2023-04-26 Released: 2024-04-24 
• Deposition Author(s): Martinez-Felices, J.M., Slotboom, D.J.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.202 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.160 (DCC) 

Starting Model: experimental

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 24.66 kDa 
• Atom Count: 1,585 
• Modeled Residue Count: 175 
• Deposited Residue Count: 199 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalamin ABC transporter	A	199	Thiobacillus denitrificans	Mutation(s): 0  Gene Names: Tbd_2719 Membrane Entity: Yes
UniProt
Find proteins for Q3SFD8 (Thiobacillus denitrificans (strain ATCC 25259 / T1)) Explore Q3SFD8  Go to UniProtKB:  Q3SFD8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12 (Subject of Investigation/LOI)	B [auth A]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
BNG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.202 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.160 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.982	α = 90
b = 95.982	β = 90
c = 77.291	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Martinez-Felices, J.M., Slotboom, D.J.

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Funding Organization	Location	Grant Number
Other government	Netherlands	--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Advisory