+Open data
-Basic information
Entry | Database: PDB / ID: 5vfz | ||||||
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Title | Integrase from mycobacterium phage Brujita | ||||||
Components | Gp33Offshore Racing Congress | ||||||
Keywords | DNA BINDING PROTEIN / Bacteriophage / Brujita / DNA-binding / Integrase | ||||||
Function / homology | Function and homology information DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / DNA recombination / symbiont entry into host cell / DNA binding Similarity search - Function | ||||||
Biological species | Mycobacterium phage Brujita (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.847 Å | ||||||
Authors | VanDemark, A.P. / Lunt, B. / Hatfull, G.F. | ||||||
Citation | Journal: To Be Published Title: Integrase from mycobacterium phage Brujita Authors: Lunt, B. / VanDemark, A.P. / Hatfull, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vfz.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vfz.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/5vfz ftp://data.pdbj.org/pub/pdb/validation_reports/vf/5vfz | 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: 36110.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium phage Brujita (virus) / Gene: 33, BRUJITA_33 / Production host: Escherichia coli (E. coli) / References: UniProt: B5U3A1 | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | ChemComp-NA / | ||
#4: Chemical | #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: 2.53 Å3/Da / Density % sol: 51.41 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris pH 7.5 5% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.847→50 Å / Num. obs: 31131 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.024 / Net I/σ(I): 40.3 |
-Processing
Software |
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Refinement | Resolution: 1.847→21.699 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.847→21.699 Å
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Refine LS restraints |
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LS refinement shell |
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