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Yorodumi- PDB-1ye5: Crystal structure of hypothetical protein of unknown function fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ye5 | ||||||
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Title | Crystal structure of hypothetical protein of unknown function from pyrococcus horikoshii OT3 | ||||||
Components | hypothetical protein PH0500 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ROSSMANN FOLD / TRNA SYNTHETASE / NUCLEOTIDE BINDING PROTEIN / PIN DOMAIN / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Jeyakanthan, J. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii. Authors: Jeyakanthan, J. / Inagaki, E. / Kuroishi, C. / 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 | 1ye5.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ye5.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ye5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ye5_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
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Full document | 1ye5_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 1ye5_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1ye5_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1ye5 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1ye5 | HTTPS FTP |
-Related structure data
Related structure data | 1v96SC S: Starting model for refinement 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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Details | THE CRYSTALLOGRAPHY ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHAINS (A AND B). BIOLOGICAL UNITS IS A HOMODIMER |
-Components
#1: Protein | Mass: 17210.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODON PLUS (DE3)-RIL / References: UniProt: O58236 #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: 2.1 Å3/Da / Density % sol: 40.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 12.5% PEG 4000, 0.1M MES BUFFER, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-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 26, 2003 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 18805 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.21 / Num. unique all: 18805 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V96 Resolution: 2→19.48 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 926739.16 / 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: 61.0083 Å2 / ksol: 0.372262 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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