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Yorodumi- PDB-1vd6: Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vd6 | ||||||
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Title | Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase complexed with Glycerol | ||||||
Components | Glycerophosphoryl Diester Phosphodiesterase | ||||||
Keywords | HYDROLASE / Glycerophosphoryl Diester Phosphodiesterase / Glycerophosphodiester Phosphodiesterase / Thermus thermophilus / HB8 / Glycerol Complex / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Ishijima, J. / Yutani, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase complexed with Glycerol Authors: Ishijima, J. / Yutani, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vd6.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vd6.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 1vd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vd6_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 1vd6_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 1vd6_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1vd6_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/1vd6 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/1vd6 | HTTPS FTP |
-Related structure data
Related structure data | 1v8eS 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 covalently bound by disulfide bond. |
-Components
#1: Protein | Mass: 24435.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) References: GenBank: 55978324, UniProt: Q53W25*PLUS, glycerophosphodiester phosphodiesterase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.65 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 8.1 Details: Ammonium sulfate, dioxane, pH 8.1, Microbatch, temperature 291K |
-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: Jun 24, 2003 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 55698 / Num. obs: 55698 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 4 / Num. unique all: 5701 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V8E Resolution: 1.3→31.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1397512.59 / 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: 51.19 Å2 / ksol: 0.367356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→31.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.38 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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