8PTD | pdb_00008ptd

The surface-exposed lipo-protein of BtuG1 in complex with cyanocobalamin.

• PDB DOI: https://doi.org/10.2210/pdb8PTD/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-14 Released: 2024-07-24 
• Deposition Author(s): Whittaker, J., Felices Martinez, J.M., Guskov, A., Slotboom, D.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.192 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: in silico

Literature

The surface-exposed lipo-protein of BtuG1 in complex with cyanocobalamin.

Whittaker, J., Guskov, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 39.38 kDa 
• Atom Count: 3,052 
• Modeled Residue Count: 343 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YncE family protein	A	343	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: BT_1490
UniProt
Find proteins for Q8A7N4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A7N4  Go to UniProtKB:  Q8A7N4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12	C [auth A]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
GOL	B [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
OH	D [auth A]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.192 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.471	α = 90
b = 147.665	β = 90
c = 116.043	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Whittaker, J., Felices Martinez, J.M., Guskov, A., Slotboom, D.J.

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Funding Organization	Location	Grant Number
Not funded	Netherlands	--

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release