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Yorodumi- PDB-1tr5: Room temperature structure of Staphylococcal nuclease variant tru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tr5 | ||||||
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Title | Room temperature structure of Staphylococcal nuclease variant truncated Delta+PHS I92E | ||||||
Components | ThermonucleaseMicrococcal nuclease | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nguyen, D.M. / Leila Reynald, R. / Gittis, A.G. / Lattman, E.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: insights into polarity of the protein interior Authors: Nguyen, D.M. / Leila Reynald, R. / Gittis, A.G. / Lattman, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tr5.cif.gz | 42.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tr5.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/1tr5 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/1tr5 | HTTPS FTP |
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-Related structure data
Related structure data | 1tqoSC 1tt2C S: Starting model for refinement C: citing same article (ref.) |
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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: 15700.994 Da / Num. of mol.: 1 Mutation: Deleteion of residues 44-49 and 145-149; point mutations G50F, V51N, I92E, P117G, H124L and S128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Foggi / Gene: NUC / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: P00644, micrococcal nuclease |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-THP / |
#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: 2.42 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, potassium phosphate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 20, 2002 / Details: mirrors (Osmic) |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25.59 Å / Num. all: 8362 / Num. obs: 8362 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.17 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 18.72 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 4.25 / Num. unique all: 814 / Rsym value: 0.153 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TQO Resolution: 2.1→25.59 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 641649.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.5421 Å2 / ksol: 0.30023 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→25.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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