+Open data
-Basic information
Entry | Database: PDB / ID: 1ou0 | ||||||
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Title | precorrin-8X methylmutase related protein | ||||||
Components | precorrin-8X methylmutase related protein | ||||||
Keywords | ISOMERASE / structural genomics / methylmutase / precorrin-8X / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermoplasma acidophilum DSM 1728 (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Cuff, M.E. / Joachimiak, A. / Korolev, S. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ou0.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ou0.ent.gz | 137.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ou0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ou0_validation.pdf.gz | 461.1 KB | Display | wwPDB validaton report |
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Full document | 1ou0_full_validation.pdf.gz | 487.8 KB | Display | |
Data in XML | 1ou0_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 1ou0_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/1ou0 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/1ou0 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | unknown; extensive D2 tetramer in asymmetric unit. |
-Components
#1: 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.88 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 150 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97891, 0.97878, 0.99187 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 7, 2002 | ||||||||||||
Radiation | Monochromator: sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 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 % |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 51.3685 Å2 / ksol: 0.344505 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.43 Å2 / Biso mean: 41.49 Å2 / Biso min: 14.46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→37.24 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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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
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