+Open data
-Basic information
Entry | Database: PDB / ID: 6sn6 | |||||||||
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Title | CARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-GLUTAMIC ACID | |||||||||
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: 1.93 Å | |||||||||
Authors | Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P. | |||||||||
Citation | Journal: To Be Published Title: CARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-GLUTAMIC ACID 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 | 6sn6.cif.gz | 157.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sn6.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 6sn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/6sn6 ftp://data.pdbj.org/pub/pdb/validation_reports/sn/6sn6 | 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: 36641.277 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-3K0 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.24 Å3/Da / Density % sol: 76.54 % |
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Crystal grow | Temperature: 294 K / Method: counter-diffusion / Details: SA 1.4 M |
-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 PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→30 Å / Num. obs: 58550 / % possible obs: 98.98 % / Redundancy: 31.59 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 14.75 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 15.13 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 6822 / % possible all: 94.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→27.93 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.799 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.067 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.49 Å2 / Biso mean: 17.73 Å2 / Biso min: 9.29 Å2
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Refinement step | Cycle: final / Resolution: 1.93→27.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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