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- PDB-1ou0: precorrin-8X methylmutase related protein -

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Basic information

Entry
Database: PDB / ID: 1ou0
Titleprecorrin-8X methylmutase related protein
Componentsprecorrin-8X methylmutase related protein
KeywordsISOMERASE / structural genomics / methylmutase / precorrin-8X / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


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 related protein
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsCuff, M.E. / Joachimiak, A. / Korolev, S. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a predicted precorrin-8x methylmutase from Thermoplasma acidophilum.
Authors: Cuff, M.E. / Miller, D.J. / Korolev, S. / Xu, X. / Anderson, W.F. / Edwards, A. / Joachimiak, A. / Savchenko, A.
History
DepositionMar 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: precorrin-8X methylmutase related protein
B: precorrin-8X methylmutase related protein
C: precorrin-8X methylmutase related protein
D: precorrin-8X methylmutase related protein


Theoretical massNumber of molelcules
Total (without water)91,3844
Polymers91,3844
Non-polymers00
Water11,295627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-60 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.450, 86.820, 120.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsunknown; extensive D2 tetramer in asymmetric unit.

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Components

#1: Protein
precorrin-8X methylmutase related protein


Mass: 22845.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Species: Thermoplasma acidophilum / Strain: DSM1728 / Gene: Ta0654 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HKE7, precorrin-8X methylmutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG3350, di-NH4 tartrate, glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 %PEG33501reservoir
20.5 Mdi-ammonium tartrate1reservoir
34 %glycerol1reservoirpH6.6

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97891, 0.97878, 0.99187
DetectorType: SBC-2 / Detector: CCD / Date: Feb 7, 2002
RadiationMonochromator: sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978911
20.978781
30.991871
ReflectionResolution: 2.1→37.24 Å / Num. all: 45241 / Num. obs: 43633 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.5 Å2 / Limit h max: 36 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 60 / Limit l min: 0 / Observed criterion F max: 443522.06 / Observed criterion F min: 0.32
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. all: 45241 / Num. obs: 43633 / % possible obs: 96.4 %

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
d*TREKdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→37.24 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4399 10.1 %random
Rwork0.202 ---
all0.205 45240 --
obs0.2027 43633 96.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 51.3685 Å2 / ksol: 0.344505 e/Å3
Displacement parametersBiso max: 97.43 Å2 / Biso mean: 41.49 Å2 / Biso min: 14.46 Å2
Baniso -1Baniso -2Baniso -3
1--8.73 Å20 Å20 Å2
2--12.48 Å20 Å2
3----3.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-50 Å
Luzzati sigma a0.29 Å0.24 Å
Luzzati d res high-2.1
Refinement stepCycle: LAST / Resolution: 2.1→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5807 0 0 627 6434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg21.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.85
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.20.324504100.2845300.0145603503489.8
2.2-2.310.31453010.30.26146330.0145569516392.7
2.31-2.460.27528100.23847660.0125580529494.9
2.46-2.650.26354910.20.23348450.0115604539496.3
2.65-2.910.2595519.90.22450000.0115642555198.4
2.91-3.330.2525559.90.21250410.0115648559699.1
3.33-4.20.20257510.10.16651240.0085704569999.9
4.2-37.240.20260710.30.17852950.0085925590299.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 37.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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