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Yorodumi- PDB-2pu3: Structural adaptation of endonuclease I from the cold-adapted and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pu3 | ||||||
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Title | Structural adaptation of endonuclease I from the cold-adapted and halophilic bacterium Vibrio salmonicida | ||||||
Components | Endonuclease I | ||||||
Keywords | HYDROLASE / cold adaptation / salt adaptation / psychrophilic enzymes / Endonuclease I | ||||||
Function / homology | Endonuclease I / Endonuclease I / endonuclease activity / metal ion binding / Endonuclease I Function and homology information | ||||||
Biological species | Vibrio salmonicida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Altermark, B. / Helland, R. / Moe, E. / Willassen, N.P. / Smalas, A.O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structural adaptation of endonuclease I from the cold-adapted and halophilic bacterium Vibrio salmonicida. Authors: Altermark, B. / Helland, R. / Moe, E. / Willassen, N.P. / Smalas, A.O. | ||||||
History |
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Remark 999 | SEQUENCE THE RESIDUE NUMBERS IN THE ENTRY FOLLOW THAT OF VIBRIO VULNIFICUS (PDB 1OUO) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pu3.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pu3.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 2pu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/2pu3 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/2pu3 | HTTPS FTP |
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-Related structure data
Related structure data | 1ouoS S: Starting model for refinement |
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Similar 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: 24583.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio salmonicida (bacteria) / Species: Aliivibrio salmonicida / Strain: LFI1238 / Plasmid: pBAD/gIII / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q2XSL7, deoxyribonuclease I | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 30 % PEG 3350, 0.1 M Tris, 0.25 M sodium acetate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0707 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 2, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0707 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.923 Å / Num. all: 31040 / Num. obs: 30823 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 10.24 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 14 / Rsym value: 0.074 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OUO Resolution: 1.5→33.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.015 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 10.917 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→33.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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