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Yorodumi- PDB-1rni: Bifunctional DNA primase/polymerase domain of ORF904 from the arc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rni | ||||||
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Title | Bifunctional DNA primase/polymerase domain of ORF904 from the archaeal plasmid pRN1 | ||||||
Components | ORF904 | ||||||
Keywords | REPLICATION / DNA polymerase / primase / polymerization / evolution of nucleic acid polymerizing enzymes | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus islandicus (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Lipps, G. / Weinzierl, A.O. / von Scheven, G. / Buchen, C. / Cramer, P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structure of a bifunctional DNA primase-polymerase Authors: Lipps, G. / Weinzierl, A.O. / Von Scheven, G. / Buchen, C. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rni.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rni.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rni_validation.pdf.gz | 414.8 KB | Display | wwPDB validaton report |
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Full document | 1rni_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 1rni_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1rni_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/1rni ftp://data.pdbj.org/pub/pdb/validation_reports/rn/1rni | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25089.746 Da / Num. of mol.: 1 / Fragment: DNA primase/polymerase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus (acidophilic) / Production host: Escherichia coli (E. coli) / References: UniProt: Q54324 |
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#2: Chemical | ChemComp-ZN / |
#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: 2.38 Å3/Da / Density % sol: 48.26 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris, sodium acetate, PEG 4000, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9192, 0.9793, 0.9797, 1.280 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2003 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→20 Å / Num. obs: 21123 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.059 | |||||||||||||||
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.228 / Num. unique all: 2085 / % possible all: 100 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 2085 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refinement | *PLUS Rfactor Rfree: 0.261 / Rfactor Rwork: 0.243 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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