+Open data
-Basic information
Entry | Database: PDB / ID: 4duk | ||||||
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Title | Carboxypeptidase T with L-BENZYLSUCCINIC ACID | ||||||
Components | Carboxypeptidase T | ||||||
Keywords | HYDROLASE | ||||||
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: 1.57 Å | ||||||
Authors | Kuznetsov, S.A. / Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P. | ||||||
Citation | Journal: Febs J. / Year: 2015 Title: Structural insights into the broad substrate specificity of carboxypeptidase T from Thermoactinomyces vulgaris. Authors: Akparov, V.K.h. / Timofeev, V.I. / Khaliullin, I.G. / Svedas, V. / Chestukhina, G.G. / 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 | 4duk.cif.gz | 168.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4duk.ent.gz | 142.1 KB | Display | PDB format |
PDBx/mmJSON format | 4duk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/4duk ftp://data.pdbj.org/pub/pdb/validation_reports/du/4duk | HTTPS FTP |
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-Related 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36958.637 Da / Num. of mol.: 1 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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-Non-polymers , 6 types, 332 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-BZS / | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: 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 | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→30 Å / Num. all: 103675 / Num. obs: 101808 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→10 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.204 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.049 / 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: 15.759 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.613 Å / Total num. of bins used: 20
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