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Yorodumi- PDB-5h0m: Crystal structure of deep-sea thermophilic bacteriophage GVE2 HNH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h0m | ||||||
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Title | Crystal structure of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease with zinc ion | ||||||
Components | HNH endonuclease | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Geobacillus virus E2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å | ||||||
Authors | Zhang, L.K. / Xu, D.D. / Huang, Y.C. / Gong, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Rep / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h0m.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h0m.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 5h0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/5h0m ftp://data.pdbj.org/pub/pdb/validation_reports/h0/5h0m | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Geobacillus virus E2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U7Q1S7*PLUS |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE HAS BEEN DEPOSITED TO DATABASE WITH ACCESSION NUMBER YP_001522898.1. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.43 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. obs: 18179 / % possible obs: 99.7 % / Redundancy: 13.7 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 65.2 |
Reflection shell | Resolution: 1.52→1.55 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 6.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.52→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.06
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.17 Å2
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Refinement step | Cycle: 1 / Resolution: 1.52→50 Å
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Refine LS restraints |
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