9FRC | pdb_00009frc

Architectural insights into spatially distinct corrin and metal binding sites of CobN

PDB DOI: https://doi.org/10.2210/pdb9FRC/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Brucella melitensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-18 Released: 2025-07-02
Deposition Author(s): Pickersgill, R.W., Brown, D.G., Ladakis, D., Warren, M.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free:
0.275 (Depositor), 0.277 (DCC)
R-Value Work:
0.184 (Depositor), 0.189 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Architecture of CobN

Pickersgill, R.W., Brown, D.G., Ladakis, D., Warren, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 42.94 kDa
Atom Count: 3,052
Modeled Residue Count: 384
Deposited Residue Count: 384
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobn protein	A	384	Brucella melitensis	Mutation(s): 0 Gene Names: BMEI0695 EC: 6.6.1.2
UniProt
Find proteins for Q8YHV1 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YHV1 Go to UniProtKB: Q8YHV1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8YHV1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IFT (Subject of Investigation/LOI) Query on A1IFT 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]	Hydrogenobyrinic acid a,c-diamide C₄₅ H₆₂ N₆ O₁₂ ZGGWTIPDUOTHRA-NREUJTCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.275 (Depositor), 0.277 (DCC)
R-Value Work: 0.184 (Depositor), 0.189 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.32	α = 90
b = 73.6	β = 90
c = 86.47	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-02

Deposition Author(s):

Pickersgill, R.W.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/001946/1

Revision History (Full details and data files)

Version 1.0: 2025-07-02
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.