+Open data
-Basic information
Entry | Database: PDB / ID: 4tr2 | |||||||||
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Title | Crystal structure of PvSUB1 | |||||||||
Components | Subtilisin-like 1 serine protease | |||||||||
Keywords | HYDROLASE / plasmodium egress protease / calcium-binding | |||||||||
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: 2.7 Å | |||||||||
Authors | Giganti, D. / Bouillon, A. / Martinez, M. / Weber, P. / Girard-Blanc, C. / Petres, S. / Haouz, A. / Barale, J.C. / Alzari, P.M. | |||||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2014 Title: A novel Plasmodium-specific prodomain fold regulates the malaria drug target SUB1 subtilase. Authors: Giganti, D. / Bouillon, A. / Tawk, L. / Robert, F. / Martinez, M. / Crublet, E. / Weber, P. / Girard-Blanc, C. / Petres, S. / Haouz, A. / Hernandez, J.F. / Mercereau-Puijalon, O. / 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 | 4tr2.cif.gz | 388.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tr2.ent.gz | 316.6 KB | Display | PDB format |
PDBx/mmJSON format | 4tr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tr2_validation.pdf.gz | 465.7 KB | Display | wwPDB validaton report |
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Full document | 4tr2_full_validation.pdf.gz | 475.3 KB | Display | |
Data in XML | 4tr2_validation.xml.gz | 33 KB | Display | |
Data in CIF | 4tr2_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/4tr2 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/4tr2 | HTTPS FTP |
-Related structure data
Related structure data | 1cgiS 1dbiS 1ea7S 1ic6S 1lw6S 1r0rS 2tecS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 73540.398 Da / Num. of mol.: 2 / Fragment: Residues 26-630 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: sub1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: E6Y8B9 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M phosphate citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→45 Å / Num. obs: 37100 / % possible obs: 99.4 % / Redundancy: 8.6 % / Biso Wilson estimate: 60.13 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software | Name: BUSTER / Version: 2.11.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2TEC, 1DBI, 1CGI, 1R0R, 1LW6, 1EA7, and 1IC6 Resolution: 2.7→45.1 Å / Cor.coef. Fo:Fc: 0.9288 / Cor.coef. Fo:Fc free: 0.8957 / SU R Cruickshank DPI: 0.537 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.541 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.294
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Displacement parameters | Biso mean: 61.98 Å2
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Refine analyze | Luzzati coordinate error obs: 0.418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.7→45.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 19
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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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