+Open data
-Basic information
Entry | Database: PDB / ID: 3v38 | ||||||
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Title | Carboxypeptidase T mutant L254N | ||||||
Components | Carboxypeptidase T | ||||||
Keywords | HYDROLASE / peptidase | ||||||
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: 1.5 Å | ||||||
Authors | Timofeev, V.I. / Kuznetsov, S.A. / Akparov, V.K. / Kuranova, I.P. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Carboxypeptidase T mutant L254N Authors: Timofeev, V.I. / Kuznetsov, S.A. / 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 | 3v38.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v38.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 3v38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/3v38 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/3v38 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 36959.582 Da / Num. of mol.: 1 / Mutation: L254N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Gene: cpt / Production host: Escherichia coli (E. coli) / References: UniProt: P29068, carboxypeptidase T | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 273 K / Method: counter diffusion / Details: COUNTER DIFFUSION, temperature 273K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 119766 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→10 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.644 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 16.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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