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Yorodumi- PDB-8coz: Structure of the catalytic domain of P. vivax Sub1 (triclinic cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8coz | ||||||
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Title | Structure of the catalytic domain of P. vivax Sub1 (triclinic crystal form) | ||||||
Components | subtilisin | ||||||
Keywords | HYDROLASE / Plasmodium / serine protease / drug target / malaria | ||||||
Function / homology | Function and homology information subtilisin / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.438 Å | ||||||
Authors | Martinez, M. / Bouillon, A. / Batista, F. / Alzari, P.M. / Barale, J.C. / Haouz, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: 3D structures of the Plasmodium vivax subtilisin-like drug target SUB1 reveal conformational changes to accommodate a substrate-derived alpha-ketoamide inhibitor. Authors: Martinez, M. / Batista, F.A. / Maurel, M. / Bouillon, A. / Ortega Varga, L. / Wehenkel, A.M. / Le Chevalier-Sontag, L. / Blondel, A. / Haouz, A. / Hernandez, J.F. / Alzari, P.M. / Barale, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8coz.cif.gz | 286.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8coz.ent.gz | 227.3 KB | Display | PDB format |
PDBx/mmJSON format | 8coz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8coz_validation.pdf.gz | 469.3 KB | Display | wwPDB validaton report |
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Full document | 8coz_full_validation.pdf.gz | 472.8 KB | Display | |
Data in XML | 8coz_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 8coz_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/8coz ftp://data.pdbj.org/pub/pdb/validation_reports/co/8coz | HTTPS FTP |
-Related structure data
Related structure data | 8coyC 8cp0C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38003.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: sub1, PVC01_100035100, PVT01_100029100, PVW1_100050600 Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: E6Y8B9, subtilisin #2: Chemical | ChemComp-CA / #3: Sugar | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.5 M LiSO4, 15% W/V PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.438→42.7 Å / Num. obs: 118611 / % possible obs: 91.2 % / Redundancy: 3.1 % / CC1/2: 0.99 / Rpim(I) all: 0.047 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.438→1.44 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5123 / CC1/2: 0.39 / Rpim(I) all: 0.794 / % possible all: 79.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.438→27.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.072
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Displacement parameters | Biso mean: 19.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.438→27.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.44→1.45 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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