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- PDB-2wcz: 1.6A resolution structure of Archaeoglobus fulgidus Hjc, a Hollid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wcz | ||||||
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Title | 1.6A resolution structure of Archaeoglobus fulgidus Hjc, a Holliday junction resolvase from an archaeal hyperthermophile | ||||||
![]() | HOLLIDAY JUNCTION RESOLVASE | ||||||
![]() | HYDROLASE / TYPE II RESTRICTION ENDONUCLEASE / DNA BINDING PROTEIN / HOLLIDAY JUNCTION RESOLVASE | ||||||
Function / homology | ![]() crossover junction endodeoxyribonuclease / crossover junction DNA endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carolis, C. / Koehler, C. / Sauter, C. / Basquin, J. / Suck, D. / Toeroe, I. | ||||||
![]() | ![]() Title: 1.6 A Resolution Structure of Archaeoglobus Fulgidus Hjc, a Holliday Junction Resolvase from an Archaeal Hyperthermophile Authors: Carolis, C. / Koehler, C. / Sauter, C. / Basquin, J. / Suck, D. / Toeroe, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.4 KB | Display | ![]() |
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PDB format | ![]() | 87.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.7 KB | Display | ![]() |
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Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wcwC ![]() 1gefS ![]() 1ipiS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.7801, 0.6249, 0.03114), Vector: |
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Components
#1: Protein | Mass: 15674.213 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-136 Source method: isolated from a genetically manipulated source Details: THE WILD-TYPE PROTEIN / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | CHLORIDE (CL): CHLORIDE ANION | Sequence details | G1, T2 (TEV PROTEASE SITE) AND G4 (NCOI RESTRICTIO | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 31 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 20% PEG3350, 200MM MGCL2, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 27, 2007 / Details: SINGLE SILICON (111) MONOCHROMATOR |
Radiation | Monochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 27133 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 10.85 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.67 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.14 / % possible all: 77.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1IPI, 1GEF Resolution: 1.65→32.299 Å / SU ML: 1.27 / σ(F): 0.03 / Phase error: 19.78 / Stereochemistry target values: ML Details: N-TERMINAL RESIDUES UPTO A5 AND B8, C-TERMINAL RESIDUES FROM A129 AND B126 ARE DISORDERED. LOOP FROM B28 TO B31 MISSING DUE TO LACK OF DENSITY RESIDUES A30-A33 HAVE WEEK ELECTRON DENSITY, ...Details: N-TERMINAL RESIDUES UPTO A5 AND B8, C-TERMINAL RESIDUES FROM A129 AND B126 ARE DISORDERED. LOOP FROM B28 TO B31 MISSING DUE TO LACK OF DENSITY RESIDUES A30-A33 HAVE WEEK ELECTRON DENSITY, THEY HAVE BEEN MODELLED FROM A MUTANT STRUCTURE 2WCW
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.462 Å2 / ksol: 0.447 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→32.299 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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