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- PDB-21vt: Crystal structure of Brucella melitensis CobT C-terminal domain w... -

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Basic information

Entry
Database: PDB / ID: 21vt
TitleCrystal structure of Brucella melitensis CobT C-terminal domain with CobT-shaft truncation
ComponentsCobaltochelatase subunit CobT
KeywordsLIGASE / Cobalt chelatase / CobT / VWA
Function / homologyCITRIC ACID
Function and homology information
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsZhou, Y.L. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471323 China
CitationJournal: Biorxiv / Year: 2026
Title: Assembly of the ATP-driven cobalt chelatase
Authors: 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.
History
DepositionDec 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cobaltochelatase subunit CobT
B: Cobaltochelatase subunit CobT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5713
Polymers60,3792
Non-polymers1921
Water11,043613
1
A: Cobaltochelatase subunit CobT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3822
Polymers30,1891
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cobaltochelatase subunit CobT


Theoretical massNumber of molelcules
Total (without water)30,1891
Polymers30,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.506, 76.630, 87.272
Angle α, β, γ (deg.)90.00, 101.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cobaltochelatase subunit CobT


Mass: 30189.492 Da / Num. of mol.: 2 / Fragment: CobT C-terminal domain with CobT-shaft truncation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Sodium citrate, PEG 4000, Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.48→57.04 Å / Num. obs: 83723 / % possible obs: 98.9 % / Redundancy: 6.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.083 / Rrim(I) all: 0.128 / Net I/σ(I): 1
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.558 / Num. unique obs: 11345 / CC1/2: 0.714 / Rpim(I) all: 0.426 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→57.04 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 4113 4.91 %
Rwork0.1627 --
obs0.1638 83686 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→57.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 13 613 4787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054318
X-RAY DIFFRACTIONf_angle_d0.8325858
X-RAY DIFFRACTIONf_dihedral_angle_d14.2941660
X-RAY DIFFRACTIONf_chiral_restr0.074668
X-RAY DIFFRACTIONf_plane_restr0.008772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.23991020.24222363X-RAY DIFFRACTION85
1.5-1.520.23291270.23312489X-RAY DIFFRACTION89
1.52-1.540.28991460.22772606X-RAY DIFFRACTION94
1.54-1.560.22651340.21062683X-RAY DIFFRACTION98
1.56-1.580.23091300.20852817X-RAY DIFFRACTION100
1.58-1.60.23871280.20092753X-RAY DIFFRACTION100
1.6-1.620.25191270.19922764X-RAY DIFFRACTION100
1.62-1.650.22561290.18672810X-RAY DIFFRACTION100
1.65-1.680.21471300.18422739X-RAY DIFFRACTION100
1.68-1.70.2131400.18532794X-RAY DIFFRACTION100
1.7-1.740.20161420.17212764X-RAY DIFFRACTION100
1.74-1.770.18841530.17442769X-RAY DIFFRACTION100
1.77-1.80.20281500.17412779X-RAY DIFFRACTION100
1.8-1.840.18941250.16822751X-RAY DIFFRACTION100
1.84-1.890.2131870.17152762X-RAY DIFFRACTION100
1.89-1.930.20671670.17312721X-RAY DIFFRACTION100
1.93-1.990.20141560.1712764X-RAY DIFFRACTION100
1.99-2.040.18441350.15562774X-RAY DIFFRACTION100
2.04-2.110.1981530.15872783X-RAY DIFFRACTION100
2.11-2.190.18191540.15962755X-RAY DIFFRACTION100
2.19-2.270.18071370.15252775X-RAY DIFFRACTION100
2.27-2.380.16491370.15452781X-RAY DIFFRACTION100
2.38-2.50.20131490.16212788X-RAY DIFFRACTION100
2.5-2.660.20291590.16052763X-RAY DIFFRACTION100
2.66-2.860.19161530.16362771X-RAY DIFFRACTION100
2.86-3.150.18171200.15792817X-RAY DIFFRACTION100
3.15-3.610.13831370.14282807X-RAY DIFFRACTION100
3.61-4.550.14411580.12782793X-RAY DIFFRACTION100
4.55-57.040.17141480.15852838X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -5.4966 Å / Origin y: -7.5317 Å / Origin z: 21.8618 Å
111213212223313233
T0.0949 Å2-0.011 Å2-0.0076 Å2-0.083 Å20.0067 Å2--0.1224 Å2
L0.3299 °2-0.1081 °2-0.3063 °2-0.2518 °20.3183 °2--1.0624 °2
S0.0112 Å °0.0089 Å °-0.0093 Å °-0.0171 Å °0.0307 Å °-0.0118 Å °0.0461 Å °0.0425 Å °-0.0453 Å °
Refinement TLS groupSelection details: all

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