8JBS

B12-binding domain from Chloracidobacterium thermophilum MerR family protein, dark state

• PDB DOI: https://doi.org/10.2210/pdb8JBS/pdb

• Classification: TRANSCRIPTION
• Organism(s): Chloracidobacterium thermophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-09 Released: 2024-11-13 
• Deposition Author(s): Zhang, S., Yu, Y.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Starting Model: in silico

Literature

SignatureFinder enables sequence mining to identify cobalamin-dependent photoreceptor proteins

Yu, Y., Jeffreys, L.N., Poddar, H., Hill, A., Johannissen, L., Dai, F., Sakuma, M., Leys, D., Heyes, D.J., Zhang, S., Scrutton, N.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.41 kDa 
• Atom Count: 3,825 
• Modelled Residue Count: 449 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cobalamin binding protein	A, B	327	Chloracidobacterium thermophilum	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12 (Subject of Investigation/LOI)	C [auth A], E [auth B]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
5AD (Subject of Investigation/LOI)	D [auth A], F [auth B]	5'-DEOXYADENOSINE C10 H13 N5 O3 XGYIMTFOTBMPFP-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.218	α = 90
b = 125.218	β = 90
c = 73.088	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Zhang, S., Yu, Y.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/S030336/1

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release