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Yorodumi- PDB-4j4n: Crystal structure of FK506 binding domain of plasmodium falciparu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j4n | ||||||
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Title | Crystal structure of FK506 binding domain of plasmodium falciparum FKBP35 in complex with D44 | ||||||
Components | FK506-binding protein (FKBP)-type peptidyl-propyl isomerase | ||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / D44 / FKBP35 / FK506 BINDING / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of phosphoprotein phosphatase activity / FK506 binding / protein peptidyl-prolyl isomerization / chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / protein dimerization activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Sreekanth, R. / Harikishore, A. / Yoon, H.S. | ||||||
Citation | Journal: Sci Rep / Year: 2013 Title: Small molecule Plasmodium FKBP35 inhibitor as a potential antimalaria agent. Authors: Harikishore, A. / Niang, M. / Rajan, S. / Preiser, P.R. / 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 | 4j4n.cif.gz | 158 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j4n.ent.gz | 127.4 KB | Display | PDB format |
PDBx/mmJSON format | 4j4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/4j4n ftp://data.pdbj.org/pub/pdb/validation_reports/j4/4j4n | HTTPS FTP |
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-Related structure data
Related structure data | 4j4oC 2vn1S 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14531.420 Da / Num. of mol.: 3 / Fragment: FK506 BINDING DOMAIN, UNP RESIDUES 1-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: FKBP35, PFL2275C / Plasmid: PETSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I4V8, peptidylprolyl isomerase #2: Chemical | #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: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 3.5M AMMONIUM SULPHATE, 0.1M CITRATE BUFFER, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9642 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2011 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9642 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. obs: 12747 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.31 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.93 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VN1 Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / SU B: 39.084 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R: 2.481 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 77.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.82 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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