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Yorodumi- PDB-3bt8: Crystal Structure of Mutant Cyclophilin (R147A) from Leishmania d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bt8 | ||||||
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Title | Crystal Structure of Mutant Cyclophilin (R147A) from Leishmania donovani | ||||||
Components | Peptidyl-prolyl cis-trans isomerase | ||||||
Keywords | ISOMERASE / CYCLOPHILIN / ROTAMASE / PROLINE / CIS-TRANS / PROTOZOA / LEISHMANIA / DONOVANI / KALA-AZAR | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Venugopal, V. / Sen, B. / Datta, A.K. / Banerjee, R. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Mutant Cyclophilin from Leishmania Donovani Authors: Venugopal, V. / Sen, B. / Datta, A.K. / Banerjee, R. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Structure of cyclophilin from Leishmania donovani at 1.97 A resolution Authors: Venugopal, V. / Sen, B. / Datta, A.K. / Banerjee, R. #2: Journal: Biochemistry / Year: 2007 Title: Amino acid residues of Leishmania donovani cyclophilin key to interaction with its adenosine kinase: biological implications Authors: Sen, B. / Venugopal, V. / Chakraborty, A. / Datta, R. / Dolai, S. / Banerjee, R. / Datta, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bt8.cif.gz | 46 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bt8.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bt8_validation.pdf.gz | 421.6 KB | Display | wwPDB validaton report |
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Full document | 3bt8_full_validation.pdf.gz | 424.9 KB | Display | |
Data in XML | 3bt8_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 3bt8_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/3bt8 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/3bt8 | HTTPS FTP |
-Related structure data
Related structure data | 2haqS 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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Unit cell |
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-Components
#1: Protein | Mass: 19004.426 Da / Num. of mol.: 1 / Fragment: UNP residues 22-187 / Mutation: R147A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (eukaryote) / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9U9R3, peptidylprolyl isomerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.02 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.01M TRIS, 10.0% PEG 3350, 0.02% AZIDE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2007 / Details: OSMIC MAXFLUX CONFOCAL MULTILAYER MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 5450 / % possible obs: 99.5 % / Redundancy: 6.15 % / Biso Wilson estimate: 4.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 6.17 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 4.2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HAQ Resolution: 2.7→17.3 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→17.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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