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Yorodumi- PDB-1vce: Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vce | ||||||
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Title | Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 | ||||||
Components | diphthine synthase | ||||||
Keywords | TRANSFERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information diphthine synthase / diphthine synthase activity / protein histidyl modification to diphthamide / methylation Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Kunishima, N. / Shimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of diphthine synthase from Pyrococcus horikoshii OT3 Authors: Kunishima, N. / Shimizu, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vce.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vce.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vce_validation.pdf.gz | 799.6 KB | Display | wwPDB validaton report |
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Full document | 1vce_full_validation.pdf.gz | 807.2 KB | Display | |
Data in XML | 1vce_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 1vce_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/1vce ftp://data.pdbj.org/pub/pdb/validation_reports/vc/1vce | HTTPS FTP |
-Related structure data
Related structure data | 2dsgC 2dshC 2dsiC 2dv3C 2dv4C 2dv5C 2dv7C 2dxvC 2dxwC 2dxxC 2e07C 2e08C 2e15C 2e16C 2e17C 2e7rC 2egbC 2eglC 2egsC 2ehcC 2ehlC 2z6rC C: citing same article (ref.) |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29894.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0725 / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: O58456, diphthine synthase #2: Chemical | ChemComp-SAH / | #3: 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: 2.92 Å3/Da / Density % sol: 57.56 % |
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Crystal grow | Temperature: 291 K / Method: microbach / pH: 5.5 Details: 3.85M Na Formate, 0.1M Acetate, pH 5.5, microbach, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97938 Å |
Detector | Type: RIGAKU JUPITER / Detector: CCD / Date: Feb 17, 2004 / Details: Mirror |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97938 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 45662 / Num. obs: 45662 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Biso Wilson estimate: 38.91 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.059 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 14 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.85 / Num. unique all: 4500 / Rsym value: 0.523 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→39.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2475497.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3075 Å2 / ksol: 0.370835 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→39.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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