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Yorodumi- PDB-7aru: L254N mutant of carboxypeptidase T from Thermoactinomyces vulgari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aru | ||||||
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Title | L254N mutant of carboxypeptidase T from Thermoactinomyces vulgaris N-sulfamoyl-L-valine | ||||||
Components | Carboxypeptidase T | ||||||
Keywords | HYDROLASE / carboxypeptidase | ||||||
Function / homology | Function and homology information carboxypeptidase T / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Thermoactinomyces vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P. | ||||||
Citation | Journal: To Be Published Title: L254N mutant of carboxypeptidase T from Thermoactinomyces vulgaris N-sulfamoyl-L-valine Authors: Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aru.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aru.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 7aru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/7aru ftp://data.pdbj.org/pub/pdb/validation_reports/ar/7aru | HTTPS FTP |
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-Related structure data
Related structure data | 3qnvS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36642.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Gene: cpt / Production host: Thermoactinomyces vulgaris (bacteria) / References: UniProt: P29068, carboxypeptidase T | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | ChemComp-NO5 / ( | ||||
#4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: counter-diffusion / Details: 1.6 Ammonium sulphate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. obs: 48369 / % possible obs: 99.89 % / Redundancy: 17.22 % / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.121 / Net I/σ(I): 4.0432 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 17.85 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.37 / Num. unique obs: 6958 / Rrim(I) all: 0.205 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QNV Resolution: 2.05→19.91 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.721 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 67.98 Å2 / Biso mean: 15.774 Å2 / Biso min: 8.74 Å2
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Refinement step | Cycle: final / Resolution: 2.05→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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