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Yorodumi- PDB-5tae: Conformational Sampling Differences across the Arrhenius Plot Bip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tae | ||||||
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Title | Conformational Sampling Differences across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin | ||||||
Components | Thermolysin | ||||||
Keywords | HYDROLASE / conformational sampling / room temperature / thermolysin / Arrhenius break | ||||||
Function / homology | Function and homology information thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus thermoproteolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.302 Å | ||||||
Authors | Dong, M. / Bahnson, B.J. | ||||||
Citation | Journal: To Be Published Title: Conformational Sampling Differences across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin Authors: Dong, M. / Bahnson, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tae.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tae.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 5tae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/5tae ftp://data.pdbj.org/pub/pdb/validation_reports/ta/5tae | HTTPS FTP |
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-Related structure data
Related structure data | 5t9iC 5t9kC 5t9qC 5tacC 5tadC 5taiC 5tajC 5takC 3dnzS C: citing same article (ref.) 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: UNP residues 233-548 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria) Gene: npr / Production host: Bacillus subtilis (bacteria) / References: UniProt: P00800, thermolysin |
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-Non-polymers , 6 types, 107 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-VAL / | #5: Chemical | ChemComp-LYS / | #6: Chemical | ChemComp-PO4 / | #7: 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: 2.42 Å3/Da / Density % sol: 49.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 1.4 M Na 2 KPO 4 pH 6.9 |
-Data collection
Diffraction | Mean temperature: 299.3 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 15389 / % possible obs: 97.9 % / Redundancy: 9.4 % / Net I/σ(I): 10 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DNZ Resolution: 2.302→34.522 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.71
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 28.463 Å2 / ksol: 0.321 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.302→34.522 Å
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Refine LS restraints |
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LS refinement shell |
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