+Open data
-Basic information
Entry | Database: PDB / ID: 1aih | ||||||
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Title | CATALYTIC DOMAIN OF BACTERIOPHAGE HP1 INTEGRASE | ||||||
Components | HP1 INTEGRASE | ||||||
Keywords | DNA INTEGRATION / RECOMBINATION | ||||||
Function / homology | Function and homology information DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA recombination / Hydrolases; Acting on ester bonds / hydrolase activity / symbiont entry into host cell / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus phage HP1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Hickman, A.B. / Waninger, S. / Scocca, J.J. / Dyda, F. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Molecular organization in site-specific recombination: the catalytic domain of bacteriophage HP1 integrase at 2.7 A resolution. Authors: Hickman, A.B. / Waninger, S. / Scocca, J.J. / Dyda, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aih.cif.gz | 147.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aih.ent.gz | 116.9 KB | Display | PDB format |
PDBx/mmJSON format | 1aih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aih_validation.pdf.gz | 404 KB | Display | wwPDB validaton report |
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Full document | 1aih_full_validation.pdf.gz | 418.9 KB | Display | |
Data in XML | 1aih_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1aih_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/1aih ftp://data.pdbj.org/pub/pdb/validation_reports/ai/1aih | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 19457.312 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 168 - 337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus phage HP1 (virus) / Genus: P2-like viruses / Strain: HP1C1 / Cell line: HAEMOPHILUS INFLUENZAE L10 / Gene: GENBANK U24159 / Plasmid: PHPC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P21442 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7.5 Details: VAPOR DIFFUSION, 15% PEG 8000, 45MM NA CAODYLATE, 34MM AMMONIUM SULFATE, 10MM TRIS-HCL, 4.5% GLYCEROL, 0.1 M MGCL., pH 7.5, vapor diffusion | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: CHESS / Beamline: F2 / Wavelength: 1.6498 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Dec 12, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6498 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 34819 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.7→2.78 Å / Redundancy: 3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5 / Rsym value: 0.18 / % possible all: 89.7 |
Reflection | *PLUS Num. measured all: 52126 |
Reflection shell | *PLUS % possible obs: 89.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 47.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.318 |