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Open data
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Basic information
Entry | Database: PDB / ID: 1czb | ||||||
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Title | ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM HEPES | ||||||
![]() | AVIAN SARCOMA VIRUS INTEGRASE | ||||||
![]() | TRANSFERASE / MIXED BETA-SHEET SURROUNDED BY ALPHA-HELICES | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / 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 / virion component / DNA integration / 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 / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lubkowski, J. / Dauter, Z. / Yang, F. / Alexandratos, J. / Merkel, G. / Skalka, A.M. / Wlodawer, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76 KB | Display | ![]() |
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PDB format | ![]() | 56.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.3 KB | Display | ![]() |
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Full document | ![]() | 422.8 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is (at least) a dimer constructed from chain A and a symmetry partner generated by the two-fold symmetry operator. |
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Components
#1: Protein | Mass: 17855.441 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN / Mutation: INS(P48, L49, R50, E51, N208, L209) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EPE / |
#3: 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 4000, 10% ISOPROPANOL, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS 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: ![]() ![]() ![]() |
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: 1.06→15 Å / Num. all: 69419 / Num. obs: 69419 / % possible obs: 90.01 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.06→1.08 Å / Redundancy: 4.2 % / Num. unique all: 2467 / % possible all: 86.7 |
Reflection | *PLUS Num. measured all: 250390 |
Reflection shell | *PLUS % possible obs: 86.7 % / Mean I/σ(I) obs: 3.2 |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.06→10 Å / Num. parameters: 1157 / Num. restraintsaints: 1443 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 1001 / Occupancy sum non hydrogen: 1189 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.06→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 0 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.347 |