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- PDB-3vuv: Crystal structure of the merozoite surface protein MSPDBL2 from P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vuv | ||||||
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Title | Crystal structure of the merozoite surface protein MSPDBL2 from P. falciparum bound to zinc | ||||||
![]() | Erythrocyte membrane protein, putative | ||||||
![]() | CELL ADHESION / Duffy Binding-Like domain / Erythrocyte Binding / Merozoite Surface / Malaria | ||||||
Function / homology | ![]() host cell surface binding / host cell surface receptor binding / cell surface / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Czabotar, P.E. / Hodder, A.N. / Clarke, O.B. / Lin, C.S. / Smith, B.J. / Cowman, A.F. | ||||||
![]() | ![]() Title: Insights into Duffy binding-like domains through the crystal structure and function of the merozoite surface protein MSPDBL2 from Plasmodium falciparum Authors: Hodder, A.N. / Czabotar, P.E. / Uboldi, A.D. / Clarke, O.B. / Lin, C.S. / Healer, J. / Smith, B.J. / Cowman, A.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.6 KB | Display | ![]() |
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PDB format | ![]() | 103.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.9 KB | Display | ![]() |
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Full document | ![]() | 427.4 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vuuC ![]() 2wauS C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 39560.375 Da / Num. of mol.: 1 / Fragment: DBL domain, UNP residues 127-460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Gene: PF10_0355 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Sequence details | AN ARTEFACT OF THE TEV CLEAVAGE SITE INTRODUCED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.59 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 20% PEG3350 0.2M sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2011 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2718 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.11→37.442 Å / Num. obs: 15702 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 | ||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WAU Resolution: 2.114→37.442 Å / SU ML: 0.27 / σ(F): 2.05 / Phase error: 27.21 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.114→37.442 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 9.1204 Å / Origin y: 6.3232 Å / Origin z: -1.3605 Å
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Refinement TLS group | Selection details: all |