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- PDB-1qgo: ANAEROBIC COBALT CHELATASE IN COBALAMIN BIOSYNTHESIS FROM SALMONE... -

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Basic information

Entry
Database: PDB / ID: 1qgo
TitleANAEROBIC COBALT CHELATASE IN COBALAMIN BIOSYNTHESIS FROM SALMONELLA TYPHIMURIUM
ComponentsANAEROBIC COBALAMIN BIOSYNTHETIC COBALT CHELATASE
KeywordsMETAL BINDING PROTEIN / COBALAMIN / VITAMIN B12 / METAL ION CHELATION / CHELATASE / COBALT PRECORRIN / CBIK
Function / homology
Function and homology information


sirohydrochlorin cobaltochelatase / sirohydrochlorin cobaltochelatase activity / anaerobic cobalamin biosynthetic process / tetrapyrrole binding / porphyrin-containing compound biosynthetic process / cobalt ion binding
Similarity search - Function
Anaerobic cobalt chelatase / Cobalt chelatase (CbiK) / Rossmann fold - #1400 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.4 Å
AuthorsSchubert, H.L. / Raux, E. / Warren, M.J. / Wilson, K.S.
Citation
Journal: Biochemistry / Year: 1999
Title: Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis.
Authors: Schubert, H.L. / Raux, E. / Wilson, K.S. / Warren, M.J.
#1: Journal: J.Bacteriol. / Year: 1997
Title: A Role for Salmonella Typhimurium Cbik in Cobalamin (Vitamin B12) and Siroheme Biosynthesis
Authors: Raux, E. / Thermes, C. / Heathcote, P. / Rambauch, A. / Warren, M.J.
History
DepositionMay 3, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Sep 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANAEROBIC COBALAMIN BIOSYNTHETIC COBALT CHELATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5624
Polymers29,2741
Non-polymers2883
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.097, 128.097, 84.765
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

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Components

#1: Protein ANAEROBIC COBALAMIN BIOSYNTHETIC COBALT CHELATASE / CBIK PROTEIN


Mass: 29273.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Description: HIS-TAGGED RECOMBINANT GENE / Gene: CBIK / Plasmid: PAR8668 / Gene (production host): CBIK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): LYSS / References: UniProt: Q05592
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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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: 3.35 Å3/Da / Density % sol: 63 %
Crystal growpH: 8.5
Details: 10-15% PEG (MW 4000), 0.2 M LI2SO4, 0.1 M TRIS PH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
210-15 %PEG40001reservoir
30.1 MTris1reservoir
40.2 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: MIRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 16699 / % possible obs: 99.5 % / Redundancy: 15 % / Biso Wilson estimate: 36.21 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4 / % possible all: 99.8
Reflection
*PLUS
Num. all: 16699 / Num. obs: 16597
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 839 5 %RANDOM
Rwork0.208 ---
obs-16597 99 %-
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 15 226 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.018
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.1956
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05

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