+Open data
-Basic information
Entry | Database: PDB / ID: 1w9h | ||||||
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Title | The Structure of a Piwi protein from Archaeoglobus fulgidus. | ||||||
Components | HYPOTHETICAL PROTEIN AF1318Hypothesis | ||||||
Keywords | NUCLEAR PROTEIN / ARGONAUTE / PIWI DOMAIN / RNAI / RISC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Parker, J.S. / Roe, S.M. / Barford, D. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Crystal Structure of a Piwi Protein Suggests Mechanisms for Sirna Recognition and Slicer Activity Authors: Parker, J.S. / Roe, S.M. / Barford, D. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w9h.cif.gz | 176.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w9h.ent.gz | 145.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/1w9h ftp://data.pdbj.org/pub/pdb/validation_reports/w9/1w9h | 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: 49302.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28951 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NI / #4: Chemical | ChemComp-CL / #5: 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: 2.6 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | pH: 4.6 Details: PROTEIN SOLUTION AT 10 MG/ML WAS MIXED WITH A SOLUTION CONTAINING 0.1 M SODIUM ACETATE PH 4.6, 0.1 M CADMIUM CHLORIDE, 30% PEG 400, 5 MM DTT. CRYSTALS COULD BE OBTAINED REPRODUCIBLY BY ...Details: PROTEIN SOLUTION AT 10 MG/ML WAS MIXED WITH A SOLUTION CONTAINING 0.1 M SODIUM ACETATE PH 4.6, 0.1 M CADMIUM CHLORIDE, 30% PEG 400, 5 MM DTT. CRYSTALS COULD BE OBTAINED REPRODUCIBLY BY STREAK SEEDING IN TO THE CRYSTALLISATION SOLUTION AFTER A 3 HOUR EQUILIBRATION. CRYSTALS APPEARED AFTER 2-3 DAYS AND GREW AFTER 5 DAYS TO A FINAL SIZE OF 0.1 MM X 0.1 MM X 0.1 MM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 7, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 143262 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 6.4 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→69.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.539 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→69.01 Å
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Refine LS restraints |
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