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- PDB-1f2v: CRYSTAL STRUCTURE ANALYSIS OF PRECORRIN-8X METHYLMUTASE OF AEROBI... -

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Basic information

Entry
Database: PDB / ID: 1f2v
TitleCRYSTAL STRUCTURE ANALYSIS OF PRECORRIN-8X METHYLMUTASE OF AEROBIC VITAMIN B12 SYNTHESIS
ComponentsPRECORRIN-8X METHYLMUTASE
KeywordsISOMERASE / alpha-beta wind / doubly wound sheet
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
Precorrin-8X methylmutase
Similarity search - Component
Biological speciesPseudomonas denitrificans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 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
DepositionMay 29, 2000Deposition 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
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: PRECORRIN-8X METHYLMUTASE


Theoretical massNumber of molelcules
Total (without water)23,2181
Polymers23,2181
Non-polymers00
Water3,963220
1
A: PRECORRIN-8X METHYLMUTASE

A: PRECORRIN-8X METHYLMUTASE


Theoretical massNumber of molelcules
Total (without water)46,4352
Polymers46,4352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3530 Å2
ΔGint-26 kcal/mol
Surface area16320 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 biological assembly is a dimer constructed from chain A and symmetry partner generated by the two-fold.

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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) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21638, precorrin-8X methylmutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, magnesium chloride, Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
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: May 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 10108 / Num. obs: 8066 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→20 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.278 / % possible all: 94.1
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Num. measured all: 26519
Reflection shell
*PLUS
% possible obs: 94.1 % / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 598 RANDOM
Rwork0.183 --
all0.183 10108 -
obs0.187 8066 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 0 220 1761
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33428
X-RAY DIFFRACTIONc_bond_d0.00603
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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