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- PDB-3pa7: Crystal structure of FKBP from plasmodium vivax in complex with t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pa7 | ||||||
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Title | Crystal structure of FKBP from plasmodium vivax in complex with tetrapeptide ALPF | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Balakrishna, A.M. / Alag, R. / Yoon, H.S. | ||||||
![]() | ![]() 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. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.3 KB | Display | ![]() |
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PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ni6C ![]() 4itzC ![]() 3ihzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 5 - 125 / Label seq-ID: 5 - 125
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Components
#1: Protein | Mass: 13971.687 Da / Num. of mol.: 2 / Fragment: residues 1-126 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: SALVADOR I / Gene: PVX_101260 / Plasmid: pSUMO / Production host: ![]() ![]() ![]() ![]() #2: Protein/peptide | | Mass: 446.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.99 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 100mM BICINE, 2.4M Ammonium sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2010 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.61→30 Å / Num. obs: 6670 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 22.03 |
Reflection shell | Resolution: 2.61→2.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.028 / Mean I/σ(I) obs: 22.03 / Num. unique all: 6660 / % possible all: 89.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3IHZ Resolution: 2.61→24.12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 1 / SU B: 35.665 / SU ML: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.483 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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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 max: 99.51 Å2 / Biso mean: 41.4839 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→24.12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 934 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.607→2.674 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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