21VT | pdb_000021vt

Crystal structure of Brucella melitensis CobT C-terminal domain with CobT-shaft truncation

PDB DOI: https://doi.org/10.2210/pdb21VT/pdb

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

Deposited: 2025-12-31 Released: 2026-07-29
Deposition Author(s): Zhou, Y.L., Liu, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.186 (Depositor), 0.186 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Assembly of the ATP-driven cobalt chelatase

Zhou, Y.L., Yuan, H., Wu, Y.C., Wang, J., Chen, H., Yao, L., Wang, M., Wang, X., Wang, J., He, C., Chen, X., Liu, L.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.07.21.739949

Macromolecule Content

Total Structure Weight: 60.57 kDa
Atom Count: 4,846
Modeled Residue Count: 534
Deposited Residue Count: 538
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobaltochelatase subunit CobT	A, B	269	Brucella melitensis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT (Subject of Investigation/LOI) Query on CIT 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]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-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: 1.48 Å
R-Value Free: 0.186 (Depositor), 0.186 (DCC)
R-Value Work: 0.163 (Depositor), 0.163 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.506	α = 90
b = 76.63	β = 101.8
c = 87.272	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32471323

Revision History (Full details and data files)

Version 1.0: 2026-07-29
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.