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Yorodumi- PDB-1v30: Crystal Structure Of Uncharacterized Protein PH0828 From Pyrococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v30 | ||||||
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Title | Crystal Structure Of Uncharacterized Protein PH0828 From Pyrococcus horikoshii | ||||||
Components | Hypothetical UPF0131 protein PH0828 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA+BETA | ||||||
Function / homology | Function and homology information gamma-glutamylaminecyclotransferase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Tajika, Y. / Sakai, N. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of hypothetical protein PH0828 from Pyrococcus horikoshii. Authors: Tajika, Y. / Sakai, N. / Tamura, T. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v30.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v30.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 1v30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/1v30 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/1v30 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14763.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O58558 |
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#2: Chemical | ChemComp-NHE / |
#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: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: Sodium Citrate , pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 18, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→17.3 Å / Num. obs: 25279 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 25.97 Å2 / Rsym value: 0.084 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.28 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→7 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: THROUGHOUT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.45 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |