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Yorodumi- PDB-3hd0: Crystal structure of Tm1865, an Endonuclease V from Thermotoga Ma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hd0 | ||||||
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Title | Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima | ||||||
Components | Endonuclease V | ||||||
Keywords | HYDROLASE / structural genomics / ISFI / RNaseH SUPERFAMILY / Endonuclease V / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / Cytoplasm / DNA damage / DNA repair / Endonuclease / Magnesium / Nuclease | ||||||
Function / homology | Function and homology information deoxyribonuclease V / deoxyribonuclease V activity / RNA endonuclease activity, producing 5'-phosphomonoesters / single-stranded RNA binding / DNA repair / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Utepbergenov, D. / Cooper, D.R. / Derewenda, U. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Tm1865, an Endonuclease V from Thermotoga Maritima Authors: Utepbergenov, D. / Cooper, D.R. / Derewenda, U. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hd0.cif.gz | 268 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hd0.ent.gz | 226.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hd0_validation.pdf.gz | 436.8 KB | Display | wwPDB validaton report |
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Full document | 3hd0_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 3hd0_validation.xml.gz | 27 KB | Display | |
Data in CIF | 3hd0_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hd0 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hd0 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Details | The biological unit is a monomer. |
-Components
#1: Protein | Mass: 27332.053 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nfi, TM_1865 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9X2H9, deoxyribonuclease V #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Crystallization drop was 1:1 mixture of protein dissolved in 20 mM Tris pH 8.5, 100 mM NaCl and 24 w/v% PEG 1500, 20% glycerol. The crystallization reservoir was 1.5 M NaCl, VAPOR DIFFUSION, ...Details: Crystallization drop was 1:1 mixture of protein dissolved in 20 mM Tris pH 8.5, 100 mM NaCl and 24 w/v% PEG 1500, 20% glycerol. The crystallization reservoir was 1.5 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97876, 0.97860, 0.97243 | ||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2007 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. obs: 17147 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 15.333 | ||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3.27 / % possible all: 99.8 |
-Phasing
Phasing | Method: MAD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing set |
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Phasing MAD set |
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Phasing MAD set site |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 1 / SU B: 26.597 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.281 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.703→2.773 Å / Total num. of bins used: 20
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