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- PDB-21vu: Crystal structure of Brucella melitensis CobT N-terminal domain c... -

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Basic information

Entry
Database: PDB / ID: 21vu
TitleCrystal structure of Brucella melitensis CobT N-terminal domain complex with CobS small domain.
Components
  • Cobaltochelatase subunit CobS
  • Cobaltochelatase subunit CobT
KeywordsLIGASE / Cobalt chelatase / CobS / CobT / AAA+
Function / homology
Function and homology information


cobaltochelatase / cobaltochelatase activity / cobalamin biosynthetic process / ATP hydrolysis activity / ATP binding
Similarity search - Function
Cobalt chelatase, CobT subunit / Cobalamin biosynthesis protein CobT VWA domain / Cobalamin biosynthesis protein CobT / Cobalamin biosynthesis protein CobT VWA domain / Cobaltochelatase subunit CobS / Cobaltochelatase subunit CobS N-terminal domain / Cobaltochelatase CobS subunit N terminal / : / : / ATPase, dynein-related, AAA domain ...Cobalt chelatase, CobT subunit / Cobalamin biosynthesis protein CobT VWA domain / Cobalamin biosynthesis protein CobT / Cobalamin biosynthesis protein CobT VWA domain / Cobaltochelatase subunit CobS / Cobaltochelatase subunit CobS N-terminal domain / Cobaltochelatase CobS subunit N terminal / : / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cobaltochelatase subunit CobT / Cobaltochelatase subunit CobS
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 CobS
H: Cobaltochelatase subunit CobT


Theoretical massNumber of molelcules
Total (without water)34,2422
Polymers34,2422
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-11 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.846, 122.846, 148.048
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Cobaltochelatase subunit CobS


Mass: 11721.355 Da / Num. of mol.: 1 / Fragment: small domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: BI318_03735 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AB36PZV1, cobaltochelatase
#2: Protein Cobaltochelatase subunit CobT


Mass: 22520.463 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: BI318_03740 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AB36PXH5, cobaltochelatase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
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: 4.08 Å3/Da / Density % sol: 69.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: sodium formate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 29064 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 44.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Net I/σ(I): 25.6
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 1.136 / Num. unique obs: 1678 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT1.20.1_4487data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→31.7 Å / SU ML: 0.3165 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1259
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2365 1411 4.86 %
Rwork0.2092 27609 -
obs0.2106 29020 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 0 111 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772358
X-RAY DIFFRACTIONf_angle_d0.85483207
X-RAY DIFFRACTIONf_chiral_restr0.0463374
X-RAY DIFFRACTIONf_plane_restr0.0089426
X-RAY DIFFRACTIONf_dihedral_angle_d5.2638333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.33191540.29162704X-RAY DIFFRACTION99.97
2.28-2.370.31261330.27362714X-RAY DIFFRACTION100
2.37-2.480.26421490.25332729X-RAY DIFFRACTION99.97
2.48-2.610.2781240.23522729X-RAY DIFFRACTION99.96
2.61-2.770.30521420.24922737X-RAY DIFFRACTION99.93
2.77-2.990.27741480.24682716X-RAY DIFFRACTION99.97
2.99-3.290.24071200.23132781X-RAY DIFFRACTION100
3.29-3.760.2351390.20942778X-RAY DIFFRACTION100
3.76-4.730.20411430.17052814X-RAY DIFFRACTION100
4.74-31.70.2051590.18472907X-RAY DIFFRACTION99.48

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