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- PDB-5h0o: Crystal structure of deep-sea thermophilic bacteriophage GVE2 HNH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h0o | ||||||
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Title | Crystal structure of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease with manganese ion | ||||||
![]() | HNH endonuclease | ||||||
![]() | HYDROLASE / Thermophilic bacteriophage / HNH Endonuclease / DNA nicking | ||||||
Function / homology | HNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease / endonuclease activity / nucleic acid binding / metal ion binding / : / HNH endonuclease![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, L.K. / Xu, D.D. / Huang, Y.C. / Gong, Y. | ||||||
![]() | ![]() Title: Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease. Authors: Zhang, L.K. / Xu, D.D. / Huang, Y.C. / Zhu, X.Y. / Rui, M.W. / Wan, T. / Zheng, X. / Shen, Y.L. / Chen, X.D. / Ma, K.S. / Gong, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.3 KB | Display | ![]() |
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PDB format | ![]() | 44.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.3 KB | Display | ![]() |
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Full document | ![]() | 417.3 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h0mSC S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 15754.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MN / |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE HAS BEEN DEPOSITED TO DATABASE WITH ACCESSION NUMBER YP_001522898.1. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 0.2M sodium chloride, pH 7.5, 25% (w/v) polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 19106 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.53→1.55 Å / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5H0M Resolution: 1.53→25.856 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→25.856 Å
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Refine LS restraints |
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LS refinement shell |
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