[English] 日本語
Yorodumi- PDB-4itz: Crystal structure of the FK506 binding domain of Plasmodium vivax... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4itz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the FK506 binding domain of Plasmodium vivax FKBP35 in complex with a tetrapeptide substrate | ||||||
Components |
| ||||||
Keywords | ISOMERASE/SUBSTRATE / plasmodium vivax / FKBP35 / Substrate / SucALPFpNA / PPIase / ISOMERASE / ISOMERASE-SUBSTRATE complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Sreekanth, R. / Yoon, H.S. | ||||||
Citation | Journal: Eukaryot Cell / Year: 2013 Title: Structural insights into substrate binding by PvFKBP35, a peptidylprolyl cis-trans isomerase from the human malarial parasite Plasmodium vivax. Authors: Alag, R. / Balakrishna, A.M. / Rajan, S. / Qureshi, I.A. / Shin, J. / Lescar, J. / Gruber, G. / Yoon, H.S. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4itz.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4itz.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 4itz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/4itz ftp://data.pdbj.org/pub/pdb/validation_reports/it/4itz | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13971.687 Da / Num. of mol.: 2 / Fragment: FK506-binding domain, UNP residues 1-126 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVX_101260 / Plasmid: PSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K8X6, peptidylprolyl isomerase #2: Protein/peptide | | Mass: 666.721 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.85M Ammonium aulphate, 0.1M MES buffer pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 2, 2012 / Details: 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: 1.65→33.5 Å / Num. obs: 27234 / % possible obs: 92.7 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 5 / Num. unique all: 1299 / % possible all: 88.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.981 Å / SU ML: 0.14 / σ(F): 1.69 / Phase error: 23.72 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→29.981 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|