5N0G

Crystal Structure of CobH T85A (precorrin-8x methyl mutase) complexed with C5 allyl-HBA

• PDB DOI: https://doi.org/10.2210/pdb5N0G/pdb

• Classification: ISOMERASE
• Organism(s): Rhodobacter capsulatus SB 1003
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2017-02-02 Released: 2018-02-14 
• Deposition Author(s): Nemoto-Smith, E.H., Lawrence, A.D., Brown, D.G., Warren, M.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.238 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 

Literature

Novel cobalamin analogues and their application in the trafficking of cobalamin in bacteria, worms and plants

Lawrence, A.D., Nemoto-Smith, E.H., Deery, E.C., Brown, D.G., Tullet, J., Brown, I.R., Howard, M., Boshoff, H.I., Barry III, C.E., Warren, M.J.

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)

Macromolecule Content

• Total Structure Weight: 22.85 kDa 
• Atom Count: 1,818 
• Modelled Residue Count: 208 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Precorrin-8X methylmutase	A	208	Rhodobacter capsulatus SB 1003	Mutation(s): 1  Gene Names: cobH, RCAP_rcc02046 EC: 5.4.1.2
UniProt
Find proteins for D5AV08 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)) Explore D5AV08  Go to UniProtKB:  D5AV08

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8F5	B [auth A]	3-[(1~{R},2~{S},3~{S},4~{Z},7~{S},8~{S},9~{Z},15~{R},17~{R},18~{R},19~{R})-2,7,18-tris(2-hydroxy-2-oxoethyl)-3,13,17-tris(3-hydroxy-3-oxopropyl)-1,2,7,12,12,15,17-heptamethyl-5-prop-2-enyl-3,8,15,18,19,21-hexahydrocorrin-8-yl]propanoic acid C47 H62 N4 O14 VXYZYIAZOLQLTR-JBBZEPTESA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.238 
• R-Value Work: 0.172 
• R-Value Observed: 0.175 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.23	α = 90
b = 66.63	β = 99.03
c = 48.92	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Nemoto-Smith, E.H., Lawrence, A.D., Brown, D.G., Warren, M.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K009249/1

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release