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Yorodumi- PDB-1v9c: Crystal Analysis of Precorrin-8x Methyl Mutase from Thermus Therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v9c | ||||||
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Title | Crystal Analysis of Precorrin-8x Methyl Mutase from Thermus Thermophilus | ||||||
Components | Precorrin-8x Methyl Mutase | ||||||
Keywords | ISOMERASE / ALPHA-BETA WIND / DOUBLY WOUND SHEET / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information precorrin-8X methylmutase / precorrin-8X methylmutase activity / cobalamin biosynthetic process Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Inagaki, E. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Crystal Analysis of Precorrin-8x Methyl Mutase from Thermus Thermophilus Authors: Inagaki, E. / Tahirov, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v9c.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v9c.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 1v9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v9c_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 1v9c_full_validation.pdf.gz | 457.5 KB | Display | |
Data in XML | 1v9c_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 1v9c_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/1v9c ftp://data.pdbj.org/pub/pdb/validation_reports/v9/1v9c | HTTPS FTP |
-Related structure data
Related structure data | 1f2vS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 23243.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET 11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83848, precorrin-8X methylmutase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #4: 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: 2.15 Å3/Da / Density % sol: 42.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: Lithium sulfate, Sodium citrate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Sep 22, 2003 / Details: mirrors |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 19430 / Num. obs: 19430 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1933 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F2V Resolution: 2.2→46.36 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 861416.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.1297 Å2 / ksol: 0.3698 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→46.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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