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Open data
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Basic information
Entry | Database: PDB / ID: 1e7l | ||||||
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Title | Endonuclease VII (EndoVII) N62D mutant from phage T4 | ||||||
![]() | RECOMBINATION ENDONUCLEASE VII | ||||||
![]() | ENDONUCLEASE / RESOLVASE / HOLLIDAY JUNCTION / DNASE | ||||||
Function / homology | ![]() endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Raaijmakers, H.C.A. / Vix, O. / Toro, I. / Suck, D. | ||||||
![]() | ![]() Title: Conformational Flexibility in T4 Endonuclease Vii Revealed by Crystallography: Implications for Substrate Binding and Cleavage Authors: Raaijmakers, H.C.A. / Toro, I. / Birkenbihl, R. / Kemper, B. / Suck, D. #1: ![]() Title: X-Ray Structure of T4 Endonuclease Vii - a DNA Junction Resolvase with a Novel Fold and Unusual Domain Swapped Dimer Architecture (in: No.6) Authors: Raaijmakers, H. / Vix, O. / Toro, I. / Golz, S. / Kemper, B. / Suck, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.7 KB | Display | ![]() |
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PDB format | ![]() | 138.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.6 KB | Display | ![]() |
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Full document | ![]() | 389.7 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 15.8 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 | BIOLOGICAL_UNIT: DIMERIC |
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Components
#1: Protein | Mass: 18174.762 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ONE ZN BOUND TO CYS 23,26,58,61 OF EACH CHAIN / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P13340, crossover junction endodeoxyribonuclease #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | CHAIN A, B ENGINEERED MUTATION ASN62ASP ASN62ASP IS AN INACTIVE MUTANT THE ENZYME CLEAVES DNA ...CHAIN A, B ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.5 Details: HANGING DROP VAPOUR DIFFUSION DROP SIZE: 1 + 1 UL PROTEIN SOLUTION: 12 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2, 10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6 WELL: 16- ...Details: HANGING DROP VAPOUR DIFFUSION DROP SIZE: 1 + 1 UL PROTEIN SOLUTION: 12 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2, 10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6 WELL: 16-18% PEG5KMME, 200 MM AMMONIUM SULPHATE, 10 MM 2-MERCAPTO-ETHANOL, 100 MM TRIS PH 4.5, ~1 MM SODIUM AZIDE, 20 MM MAGNESIUM ACETATE | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→27 Å / Num. obs: 81068 / % possible obs: 96.5 % / Redundancy: 2.99 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.32→1.37 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.301 / % possible all: 88.9 |
Reflection | *PLUS Lowest resolution: 27 Å / Num. measured all: 243182 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 88.9 % / Rmerge(I) obs: 0.301 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→35 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 35 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |