+Open data
-Basic information
Entry | Database: PDB / ID: 1cz9 | ||||||
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Title | ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN (D64N) FROM CITRATE | ||||||
Components | AVIAN SARCOMA VIRUS INTEGRASE | ||||||
Keywords | TRANSFERASE / MIXED BETA-SHEET SURROUNDED BY ALPHA-HELICES | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / virion component / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Avian sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.2 Å | ||||||
Authors | Lubkowski, J. / Dauter, Z. / Yang, F. / Alexandratos, J. / Merkel, G. / Skalka, A.M. / Wlodawer, A. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Atomic resolution structures of the core domain of avian sarcoma virus integrase and its D64N mutant. Authors: Lubkowski, J. / Dauter, Z. / Yang, F. / Alexandratos, J. / Merkel, G. / Skalka, A.M. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cz9.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cz9.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 1cz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cz9_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 1cz9_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 1cz9_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1cz9_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/1cz9 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/1cz9 | 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: 17854.455 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN / Mutation: D64N, INS(P48, L49, R50, E51, N208, L209) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Avian sarcoma virus / Genus: Alpharetrovirus / Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli) / References: UniProt: P03354, UniProt: O92956*PLUS |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CIT / |
#4: Water | ChemComp-HOH / |
Sequence details | THE APPARENT DISCREPANCY BETWEEN THE SEQUENCE PRESENTED HERE AND THE "POL_RSVP" SEQUENCE IS A ...THE APPARENT DISCREPANC |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.37 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 20% PEG 4000, 10% ISOPROPANOL, 100 MM CITRATE PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: Bujacz, G., (1995) J. Mol. Biol., 253, 333. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. all: 53915 / Num. obs: 53856 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 4.2 % / % possible all: 90.4 |
Reflection | *PLUS Num. obs: 53915 / Num. measured all: 345764 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 90.4 % / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.2→10 Å / Num. parameters: 1209 / Num. restraintsaints: 1445 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 939 / Occupancy sum non hydrogen: 1218 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 0 / Rfactor Rfree: 0.15 / Rfactor Rwork: 0.146 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.343 |