5N0G | pdb_00005n0g

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.172 (Depositor), 0.192 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5AV08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8F5 Query on 8F5 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.172 (Depositor), 0.192 (DCC)
R-Value Observed: 0.175 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-14

Deposition Author(s):

Nemoto-Smith, E.H.

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

Revision History (Full details and data files)

Version 1.0: 2018-02-14
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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