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- PDB-4f1j: Crystal structure of the MG2+ loaded VWA domain of plasmodium fal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f1j | ||||||
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Title | Crystal structure of the MG2+ loaded VWA domain of plasmodium falciparum trap protein | ||||||
![]() | Thrombospondin related anonymous protein | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pihlajamaa, T. / Knuuti, J. / Kajander, T. / Sharma, A. / Permi, P. | ||||||
![]() | ![]() Title: Structure of Plasmodium falciparum TRAP (thrombospondin-related anonymous protein) A domain highlights distinct features in apicomplexan von Willebrand factor A homologues. Authors: Pihlajamaa, T. / Kajander, T. / Knuuti, J. / Horkka, K. / Sharma, A. / Permi, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.8 KB | Display | ![]() |
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PDB format | ![]() | 80.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 22766.244 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: THROMBOSPONDIN RELATED ANONYMOUS PROTEIN (TRAP), TRAP / Plasmid: pRAT4 / Production host: ![]() ![]() ![]() |
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-Non-polymers , 5 types, 416 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-EDO / ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.1M BIS-TRIS, 0.2M MAGNESIUM SULFATE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2010 Details: THE OPTICAL ELEMENTS CONSIST OF A VERTICALLY COLLIMATING MIRROR (M1, FOCUS AT INFINITY) FOLLOWED BY A BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS (DCCM) IN (+--+) GEOMETRY, AND A ...Details: THE OPTICAL ELEMENTS CONSIST OF A VERTICALLY COLLIMATING MIRROR (M1, FOCUS AT INFINITY) FOLLOWED BY A BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS (DCCM) IN (+--+) GEOMETRY, AND A TOROIDAL MIRROR (M2) TO VERTICALLY AND HORIZONTALLY FOCUS THE BEAM AT THE SAMPLE POSITION (WITH 2:1 HORIZONTAL DEMAGNIFICATION) |
Radiation | Monochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.73→50 Å / Num. all: 84445 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.271 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.72 |
Reflection shell | Resolution: 1.73→1.83 Å / Redundancy: 10 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2.9 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: 11.147 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→30 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 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.73→1.773 Å / Total num. of bins used: 20
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