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Yorodumi- PDB-2qer: Crystal structure of Cryptosporidium parvum cyclophilin type pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qer | ||||||
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Title | Crystal structure of Cryptosporidium parvum cyclophilin type peptidyl-prolyl cis-trans isomerase cgd2_1660 in the presence of dipeptide ala-pro | ||||||
Components | Cyclophilin-like protein, putative | ||||||
Keywords | ISOMERASE / cryptosporidium / parvum / malaria / cyclophilin / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information catalytic step 2 spliceosome / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity Similarity search - Function | ||||||
Biological species | Cryptosporidium parvum Iowa II (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Wernimont, A.K. / Lew, J. / Hills, T. / Hassanali, A. / Lin, L. / Wasney, G. / Zhao, Y. / Kozieradzki, I. / Vedadi, M. / Schapira, M. ...Wernimont, A.K. / Lew, J. / Hills, T. / Hassanali, A. / Lin, L. / Wasney, G. / Zhao, Y. / Kozieradzki, I. / Vedadi, M. / Schapira, M. / Bochkarev, A. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Hui, R. / Artz, J.D. / Amani, M. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Cryptosporidium parvum cyclophilin type peptidyl-prolyl cis-trans isomerase cgd2_1660 in the presence of dipeptide ala-pro. Authors: Wernimont, A.K. / Lew, J. / Hills, T. / Hassanali, A. / Lin, L. / Wasney, G. / Zhao, Y. / Kozieradzki, I. / Vedadi, M. / Schapira, M. / Bochkarev, A. / Edwards, A.M. / Arrowsmith, C.H. / ...Authors: Wernimont, A.K. / Lew, J. / Hills, T. / Hassanali, A. / Lin, L. / Wasney, G. / Zhao, Y. / Kozieradzki, I. / Vedadi, M. / Schapira, M. / Bochkarev, A. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Hui, R. / Artz, J.D. / Amani, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qer.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qer.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/2qer ftp://data.pdbj.org/pub/pdb/validation_reports/qe/2qer | HTTPS FTP |
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-Related structure data
Related structure data | 2poeS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20868.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote) Species: Cryptosporidium parvum / Strain: Iowa type II / Gene: cgd2_1660 / Plasmid: pET15_TEV/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5a / References: UniProt: A3FQ68 |
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-Non-polymers , 5 types, 126 molecules
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-ALA / | ||
#4: Chemical | ChemComp-PRO / | ||
#5: Chemical | #6: 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: 3.53 Å3/Da / Density % sol: 65.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 3350, 0.1 M Ammonium sulfate, 0.1 M Tris-HCl pH 8.5, 30 mM ala-pro, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. all: 16658 / Num. obs: 16658 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.066 / Rsym value: 0.046 / Net I/σ(I): 53.7 |
Reflection shell | Resolution: 2.17→2.25 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 6.2 / Num. unique all: 1608 / Rsym value: 0.418 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2POE Resolution: 2.17→24.78 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.415 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.165 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.425 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→24.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.226 Å / Total num. of bins used: 20
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