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Yorodumi- PDB-8qvo: L211Q, L254N, T262G mutant of carboxypeptidase T from Thermoactin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qvo | ||||||
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Title | L211Q, L254N, T262G mutant of carboxypeptidase T from Thermoactinomyces vulgaris | ||||||
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: 1.96 Å | ||||||
Authors | Timofeev, V.I. / Dorovatovskii, P.V. / Lazarenko, V.A. / Akparov, V.K. / Kuranova, I.P. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: L211Q, L254N, T262G mutant of carboxypeptidase T from Thermoactinomyces vulgaris Authors: Timofeev, V.I. / Dorovatovskii, P.V. / Lazarenko, V.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 | 8qvo.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qvo.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 8qvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qvo_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 8qvo_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 8qvo_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 8qvo_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/8qvo ftp://data.pdbj.org/pub/pdb/validation_reports/qv/8qvo | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 36613.141 Da / Num. of mol.: 1 / Mutation: L211Q,L254N,T262G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Gene: cpt / Production host: Thermoactinomyces vulgaris (bacteria) / References: UniProt: P29068 | ||||||
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#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | #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: vapor diffusion, hanging drop / Details: 1.4 SA |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.75268 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75268 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→30 Å / Num. obs: 110357 / % possible obs: 99.97 % / Redundancy: 12.09 % / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.115 / Net I/σ(I): 5.8757 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 9.41 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 15903 / Rrim(I) all: 0.376 / % possible all: 99.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→28.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.51 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 14.85 Å2
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Refinement step | Cycle: 1 / Resolution: 1.96→28.91 Å
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Refine LS restraints |
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