+Open data
-Basic information
Entry | Database: PDB / ID: 1wr2 | ||||||
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Title | Crystal structure of PH1788 from Pyrococcus horikoshii Ot3 | ||||||
Components | hypothetical protein PH1789Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyrococcus horikoshii / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Sugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of PH1788 from Pyrococcus horikoshii Ot3 Authors: Sugahara, M. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wr2.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wr2.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/1wr2 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/1wr2 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26875.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O59452 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.5 / Details: JAM, pH 6.5, microbatch, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→40 Å / Num. all: 18934 / Num. obs: 18934 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.04 / Net I/σ(I): 13.6 | ||||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1852 / Rsym value: 0.647 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→37.67 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→37.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.031
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