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Yorodumi- PDB-2gju: Crystal structure of hypothetical protein PH1004 from Pyrococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gju | ||||||
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Title | Crystal structure of hypothetical protein PH1004 from Pyrococcus horikoshii OT3 | ||||||
Components | 252aa long hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / BETA BARREL / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Phosphoesterase MJ0912 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta / PHOSPHATE ION / Calcineurin-like phosphoesterase domain-containing protein Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yamamoto, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Crystal structure of hypothetical protein PH1004 from Pyrococcus horikoshii OT3 Authors: Yamamoto, H. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gju.cif.gz | 233.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gju.ent.gz | 186.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gju_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 2gju_full_validation.pdf.gz | 476.9 KB | Display | |
Data in XML | 2gju_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 2gju_validation.cif.gz | 72.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/2gju ftp://data.pdbj.org/pub/pdb/validation_reports/gj/2gju | HTTPS FTP |
-Related structure data
Related structure data | 1nnwS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | Biological assembly is dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 28678.295 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58732 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-PO4 / #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: 3.1 Å3/Da / Density % sol: 60.26 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: 0.05M Potassium dihydrogen phosphate, 10% PEG 8000, MICROBATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 18, 2005 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 93428 / Num. obs: 91840 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.086 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.6 / Num. unique all: 8949 / Rsym value: 0.256 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NNW Resolution: 2→39.43 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3998810.95 / 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: 52.6816 Å2 / ksol: 0.348221 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→39.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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