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Yorodumi- PDB-3ihz: Crystal structure of the FK506 binding domain of Plasmodium vivax... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ihz | ||||||
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Title | Crystal structure of the FK506 binding domain of Plasmodium vivax FKBP35 in complex with FK506 | ||||||
Components | 70 kDa peptidylprolyl isomerase, putative | ||||||
Keywords | ISOMERASE / Plasmodium vivax / FKBP35 / FK506 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Qureshi, I.A. / Alag, R. / Yoon, H.S. / Lescar, J. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: NMR and crystallographic structures of the FK506 binding domain of human malarial parasite Plasmodium vivax FKBP35 Authors: Alag, R. / Qureshi, I.A. / Bharatham, N. / Shin, J. / Lescar, J. / Yoon, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ihz.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ihz.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ihz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/3ihz ftp://data.pdbj.org/pub/pdb/validation_reports/ih/3ihz | HTTPS FTP |
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-Related structure data
Related structure data | 2vn1S 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: 13971.687 Da / Num. of mol.: 2 / Fragment: FK506-binding domain, residues 1-126 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Strain: Salvador I / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K8X6 #2: Chemical | ChemComp-FK5 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 100mM BICINE pH 9.0, 2.4M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 8, 2009 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→21.22 Å / Num. all: 28738 / Num. obs: 28288 / Observed criterion σ(I): 2354.8 / Redundancy: 4.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.029 / Rsym value: 0.029 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 8.2 / Num. unique all: 3782 / Rsym value: 0.15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2VN1 Resolution: 1.67→21.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.819 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.114 / 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: 20.859 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→21.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.713 Å / Total num. of bins used: 20
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