+Open data
-Basic information
Entry | Database: PDB / ID: 1en7 | ||||||
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Title | ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4 | ||||||
Components | RECOMBINATION ENDONUCLEASE VII | ||||||
Keywords | HYDROLASE / ENDONUCLEASE / RESOLVASE / HOLLIDAY JUNCTION / DNASE | ||||||
Function / homology | Function and homology information endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.4 Å | ||||||
Authors | Raaijmakers, H. / Vix, O. / Toro, I. / Suck, D. | ||||||
Citation | Journal: EMBO J. / Year: 1999 Title: X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture. Authors: Raaijmakers, H. / Vix, O. / Toro, I. / Golz, S. / Kemper, B. / Suck, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1en7.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1en7.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 1en7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1en7_validation.pdf.gz | 376.5 KB | Display | wwPDB validaton report |
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Full document | 1en7_full_validation.pdf.gz | 383.3 KB | Display | |
Data in XML | 1en7_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1en7_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/1en7 ftp://data.pdbj.org/pub/pdb/validation_reports/en/1en7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18173.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ONE ZN BOUND TO CYS 23,26,58,61 OF EACH CHAIN CA LIGANDED TO ASP40 AND ASN 62 Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: GP49 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P13340, crossover junction endodeoxyribonuclease #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 57.01 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.2 Details: HANGING DROP VAPOUR DIFFUSION 1 + 1 UL OF PROTEIN SOLUTION: 16 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2, 10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6.5; WELL: 16-18% ...Details: HANGING DROP VAPOUR DIFFUSION 1 + 1 UL OF PROTEIN SOLUTION: 16 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2, 10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6.5; WELL: 16-18% PEG 5000 MME, 200 MM CACL2, 20 MM AMMONIUM SULPHATE, 10 MM 2-MERCAPTO-ETHANOL, 100 MM TRIS PH 8.2, ~ 1 MM SODIUM AZIDE, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃Details: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: NI COATED MIRRORS |
Radiation | Monochromator: NI COATED MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→44.281 Å / Num. obs: 17578 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.81 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.33→2.46 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.253 / % possible all: 99.3 |
Reflection | *PLUS Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.253 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: ENDOVII N62D MUTANT Resolution: 2.4→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 46.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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