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Open data
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Basic information
Entry | Database: PDB / ID: 4oq2 | ||||||
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Title | 5hmC specific restriction endonuclease PvuRTs1I | ||||||
![]() | Restriction endonuclease PvuRts1 I | ||||||
![]() | HYDROLASE / cytosine hydroxymethylation / PD-(D/E)XK nuclease domain / SRA DNA binding domain / restriction endonuclease / 5-hydroxymethylcytosine / DNA | ||||||
Function / homology | SET and RING associated domain / : / SET and RING associated domain / Restriction endonuclease PvuRts1 I-like, N-terminal / endonuclease activity / Restriction endonuclease PvuRts1 I![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kazrani, A.A. / Kowalska, M. / Czapinska, H. / Bochtler, M. | ||||||
![]() | ![]() Title: Crystal structure of the 5hmC specific endonuclease PvuRts1I. Authors: Kazrani, A.A. / Kowalska, M. / Czapinska, H. / Bochtler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.8 KB | Display | ![]() |
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PDB format | ![]() | 113.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.9 KB | Display | ![]() |
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Full document | ![]() | 443.4 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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 | THE WILD-TYPE PROTEIN IS A DIMER. THE N-TERMINAL HISTIDINE TAG MAY FAVOR THE MONOMERIC FORM FOUND IN OUR CRYSTALS. |
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Components
#1: Protein | Mass: 35864.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q52612, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters |
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#2: Chemical | ChemComp-EPE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% w/v PEG4000, 20% v/v glycerol, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine, 0.1 M MOPS/HEPES sodium, pH 7.5, for ...Details: 10% w/v PEG4000, 20% v/v glycerol, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine, 0.1 M MOPS/HEPES sodium, pH 7.5, for cryoprotection, crystals were transferred to a variant of the buffer with 28% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 17509 / Num. obs: 17509 / % possible obs: 96.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1275 / Rsym value: 0.97 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED. THE LOOP FOLLOWING THE ACTIVE SITE (RESIDUES 70-76) HAS BEEN MODELED TENTATIVELY BUT IT IS MOST LIKELY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED. THE LOOP FOLLOWING THE ACTIVE SITE (RESIDUES 70-76) HAS BEEN MODELED TENTATIVELY BUT IT IS MOST LIKELY DISORDERED DUE TO THE ABSENCE OF CATALYTIC METAL IONS AND/OR TARGET DNA.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.387 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→43.83 Å
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Refine LS restraints |
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