[English] 日本語
Yorodumi- PDB-2fu0: Plasmodium falciparum cyclophilin PFE0505w putative cyclosporin-b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fu0 | ||||||
---|---|---|---|---|---|---|---|
Title | Plasmodium falciparum cyclophilin PFE0505w putative cyclosporin-binding domain | ||||||
Components | cyclophilin, putative | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / cyclophilin / PFE0505w / cyclosporin-binding domain / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information cyclosporin A binding / protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dong, A. / Lew, J. / Sundararajan, E. / Zhao, Y. / Wasney, G. / Vedadi, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. ...Dong, A. / Lew, J. / Sundararajan, E. / Zhao, Y. / Wasney, G. / Vedadi, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Hills, T. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2fu0.cif.gz | 48.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2fu0.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 2fu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fu0_validation.pdf.gz | 403.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2fu0_full_validation.pdf.gz | 403.6 KB | Display | |
Data in XML | 2fu0_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 2fu0_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/2fu0 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/2fu0 | HTTPS FTP |
-Related structure data
Related structure data | 1txjC 1xccC 1y6zC 1z6gC 1z7dC 1z81C 1zo2C 2a22C 2a4aC 2aifC 2amxC 2aqwC 2av4C 2awpC 2ayvC 2b71SC 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18188.697 Da / Num. of mol.: 1 / Fragment: residues 589-747 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus Ril References: GenBank: 23613125, UniProt: Q8I402*PLUS, peptidylprolyl isomerase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.59 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 2000 MME 0.2 M Trimethylamine N-oxide, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2006 / Details: VeriMax HR |
Radiation | Monochromator: Rigaku VeriMax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 12434 / Num. obs: 12434 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.7 / Num. unique all: 502 / Rsym value: 0.234 / % possible all: 82.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B71 Resolution: 1.8→37.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.237 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.781 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→37.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
|