+Open data
-Basic information
Entry | Database: PDB / ID: 1z81 | ||||||
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Title | Crystal Structure of cyclophilin from Plasmodium yoelii. | ||||||
Components | cyclophilin | ||||||
Keywords | ISOMERASE / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding Similarity search - Function | ||||||
Biological species | Plasmodium yoelii yoelii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Mulichak, A. / Alam, Z. / Amani, M. / Lew, J. / Wasney, G. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Hui, R. ...Mulichak, A. / Alam, Z. / Amani, M. / Lew, J. / Wasney, G. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Hui, R. / Vedadi, M. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2007 Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z81.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z81.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 1z81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/1z81 ftp://data.pdbj.org/pub/pdb/validation_reports/z8/1z81 | HTTPS FTP |
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-Related structure data
Related structure data | 1txjC 1xccC 1y6zC 1z6gC 1z7dC 1zo2C 2a22C 2a4aC 2aifC 2amxC 2aqwC 2av4C 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2fu0C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C 1mzwS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | Biological assembly is monomer of asymmetric unit. |
-Components
#1: Protein | Mass: 25968.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium yoelii yoelii (eukaryote) / Species: Plasmodium yoelii / Strain: yoelii Plasmid: pET-28a vector customized for thrombin cleavage and LIC. Production host: Escherichia coli (E. coli) / References: UniProt: Q7RSH5, 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: 3.11 Å3/Da / Density % sol: 60.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ammonium sulfate, lithium chloride, Tris HCl buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 6, 2005 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 9050 / Num. obs: 9050 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.059 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 10 % / Num. unique all: 884 / Rsym value: 0.33 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MZW Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Side chain atoms for following residues were unobserved in electron density maps and were omitted from final model: Thr25, Tyr29, Asn33, Ser39, Lys68, Lys82, Val83, Asn84, Asn85, Leu86, ...Details: Side chain atoms for following residues were unobserved in electron density maps and were omitted from final model: Thr25, Tyr29, Asn33, Ser39, Lys68, Lys82, Val83, Asn84, Asn85, Leu86, Ser115, Glu123, Lys124, Lys167, Lys 197, Glu206
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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