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- PDB-1i1h: CRYSTAL STRUCTURE ANALYSIS OF PRECORRIN-8X METHYLMUTASE COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1i1h
TitleCRYSTAL STRUCTURE ANALYSIS OF PRECORRIN-8X METHYLMUTASE COMPLEX WITH HYDROGENOBYRINIC ACID
ComponentsPRECORRIN-8X METHYLMUTASE
KeywordsISOMERASE / Precorrin / Vitamin B12
Function / homology
Function and homology information


precorrin-8X methylmutase / 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
HYDROGENOBYRINIC ACID / Precorrin-8X methylmutase
Similarity search - Component
Biological speciesPseudomonas denitrificans (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsShipman, L.W. / Li, D. / Roessner, C.A. / Scott, A.I. / Sacchettini, J.C.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of precorrin-8x methyl mutase.
Authors: Shipman, L.W. / Li, D. / Roessner, C.A. / Scott, A.I. / Sacchettini, J.C.
History
DepositionFeb 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: PRECORRIN-8X METHYLMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0982
Polymers23,2181
Non-polymers8811
Water2,108117
1
A: PRECORRIN-8X METHYLMUTASE
hetero molecules

A: PRECORRIN-8X METHYLMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1974
Polymers46,4352
Non-polymers1,7622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area7150 Å2
ΔGint-52 kcal/mol
Surface area15080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.100, 36.600, 60.300
Angle α, β, γ (deg.)90.00, 113.80, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the functional dimer is generated by the crystallographic two-fold axis: -x, y, -z

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Components

#1: Protein PRECORRIN-8X METHYLMUTASE / COBH


Mass: 23217.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas denitrificans (bacteria) / Gene: COBH / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL(21)DE3 / References: UniProt: P21638, precorrin-8X methylmutase
#2: Chemical ChemComp-COJ / HYDROGENOBYRINIC ACID


Mass: 880.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H60N4O14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Magnesium Chloride, Tris-HCl, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 299.0K
Crystal
*PLUS
Density % sol: 37 %
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
225-32.5 %PEG40001reservoir
30.2 M1reservoirMgCl2
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 20, 1999 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 17886 / Num. obs: 5501 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.266 / % possible all: 94.4
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Num. measured all: 17886
Reflection shell
*PLUS
% possible obs: 98.4 % / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.218 438 RANDOM
Rwork0.227 --
all0.227 4076 -
obs0.227 3638 -
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 63 117 1720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.43
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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