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- PDB-1w8k: Crystal structure of apical membrane antigen 1 from Plasmodium vivax -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w8k | ||||||
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Title | Crystal structure of apical membrane antigen 1 from Plasmodium vivax | ||||||
![]() | APICAL MEMBRANE ANTIGEN 1 | ||||||
![]() | ANTIGEN / PLASMODIUM ANTIGEN / MALARIA VACCINE CANDIDATE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pizarro, J.C. / Vulliez-Le Normand, B. / Chesne-Seck, M.-L. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A. | ||||||
![]() | ![]() Title: Crystal Structure of the Malaria Vaccine Candidate Apical Membrane Antigen 1 Authors: Pizarro, J.C. / Vulliez-Le Normand, B. / Chesne-Seck, M.-L. / Collins, C. / Withers-Martinez, C. / Hackett, F. / Blackman, M. / Faber, B. / Remarque, E. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.4 KB | Display | ![]() |
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PDB format | ![]() | 71.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443 KB | Display | ![]() |
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Full document | ![]() | 450.4 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 51597.047 Da / Num. of mol.: 1 / Fragment: ECTOPLASMIC REGION, RESIDUES 1-445 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: SAL I / Production host: ![]() |
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#2: Chemical | ChemComp-IMD / |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED MUTATION IN CHAIN A, SER 178 TO ASN ENGINEERED MUTATION IN CHAIN A, ASN 226 TO ASP ...ENGINEERED |
Sequence details | SEQUENCE EXPRESSED COMPRISES RESIDUES 1 TO 445. MUTATIONS S136N, N184D AND N399Q HAVE BEEN ...SEQUENCE EXPRESSED COMPRISES RESIDUES 1 TO 445. MUTATIONS S136N, N184D AND N399Q HAVE BEEN INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | pH: 7 Details: THE CRYSTALLISATION MIXTURE CONSISTED OF 10-12% (W/V) PEG3350, 100-200MM IMIDAZOLE, PH 7.0, 5-10% (V/V) ISOPROPANOL, AND 1% (V/V) DMF OR 3% (V/V) T-BUTANOL. THE PROTEIN SOLUTION WAS DILUTED ...Details: THE CRYSTALLISATION MIXTURE CONSISTED OF 10-12% (W/V) PEG3350, 100-200MM IMIDAZOLE, PH 7.0, 5-10% (V/V) ISOPROPANOL, AND 1% (V/V) DMF OR 3% (V/V) T-BUTANOL. THE PROTEIN SOLUTION WAS DILUTED BY 40 - 60% REMARK 280 WITH THE CRYSTALLISATION BUFFER, GIVING A FINAL REMARK 280 CONCENTRATION OF 4-6 MG. ML-1 IN SUSPENDED DROPS OF VOLUME REMARK 280 2 - 3 PERCENT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 152093 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING SEGMENTS WERE NOT MODELLED A171 TO 176, A204 TO A206, A210 TO A215, A297 TO A334, A403 TO A413, A476 TO A487.
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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: 41.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.34 Å
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Refine LS restraints |
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