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- PDB-2afr: The Crystal Structure of Putative Precorrin Isomerase CbiC in Cob... -

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Basic information

Entry
Database: PDB / ID: 2afr
TitleThe Crystal Structure of Putative Precorrin Isomerase CbiC in Cobalamin Biosynthesis
Componentscobalamin biosynthesis precorrin isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


cobalt-precorrin-8 methylmutase / cobalt-precorrin-8 methylmutase activity / precorrin-8X methylmutase activity / cobalamin biosynthetic process
Similarity search - Function
Cobalamin biosynthesis CobH/CbiC, precorrin-8X methylmutase / Cobalamin biosynthesis precorrin-8X methylmutase CobH/CbiC / Precorrin-8X methylmutase CobH/CbiC superfamily / Precorrin-8X methylmutase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cobalt-precorrin-8 methylmutase
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXue, Y. / Wei, Z. / Li, X.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: The crystal structure of putative precorrin isomerase CbiC in cobalamin biosynthesis
Authors: Xue, Y. / Wei, Z. / Li, X. / Gong, W.
History
DepositionJul 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cobalamin biosynthesis precorrin isomerase


Theoretical massNumber of molelcules
Total (without water)25,8881
Polymers25,8881
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: cobalamin biosynthesis precorrin isomerase

A: cobalamin biosynthesis precorrin isomerase


Theoretical massNumber of molelcules
Total (without water)51,7762
Polymers51,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area2910 Å2
ΔGint-22 kcal/mol
Surface area18310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.885, 55.885, 142.551
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein cobalamin biosynthesis precorrin isomerase


Mass: 25887.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EXP7, precorrin-8X methylmutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.48145 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ethanol, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→45.8 Å / Num. all: 10964 / Num. obs: 10964 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.8 Å2
Reflection shellResolution: 2.3→2.35 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 302183.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1100 10.2 %RANDOM
Rwork0.224 ---
all0.23 10964 --
obs0.224 10732 88.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.1831 Å2 / ksol: 0.34208 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å22.25 Å20 Å2
2--1.27 Å20 Å2
3----2.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 0 75 1729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 187 9.8 %
Rwork0.205 1717 -
obs--96.6 %

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