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- PDB-2j4w: Structure of a Plasmodium vivax apical membrane antigen 1-Fab F8.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j4w | |||||||||
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Title | Structure of a Plasmodium vivax apical membrane antigen 1-Fab F8.12.19 complex | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Igonet, S. / Vulliez-Le Normand, B. / Faure, G. / Riottot, M.M. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A. | |||||||||
![]() | ![]() Title: Cross-Reactivity Studies of an Anti-Plasmodium Vivax Apical Membrane Antigen 1 Monoclonal Antibody: Binding and Structural Characterisation. Authors: Igonet, S. / Vulliez-Le Normand, B. / Faure, G. / Riottot, M.M. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A. #1: ![]() Title: Crystal Structure of the Malaria Vaccine Candidate Apical Membrane Antigen 1 Authors: Pizarro, J.C. / Vulliez-Lenormand, B. / Chesne-Seck, M.L. / Collins, C.R. / Withers-Martinez, C. / Hackett, F. / Blackman, M.J. / Faber, B.W. / Remarque, E.J. / 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 | ![]() | 118.2 KB | Display | ![]() |
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PDB format | ![]() | 85.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2j5lC ![]() 1w8kS ![]() 2igfS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 51361.934 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: SAL I / Plasmid: PHIL-S1 / Production host: ![]() ![]() |
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#2: Antibody | Mass: 24189.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA / Source: (natural) ![]() ![]() ![]() |
#3: Antibody | Mass: 23285.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA / Source: (natural) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / ![]() |
Compound details | ENGINEERED RESIDUE IN CHAIN D, SER 136 TO ASN ENGINEERED RESIDUE IN CHAIN D, ASN 184 TO ASP ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.63 % |
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Crystal grow![]() | pH: 4.4 Details: PVAMA1 AND FAB-F8.12.19 WERE MIXED IN A 1:1 STOICHIOMETRIC RATIO AND LEFT TO INCUBATE FOR 4 HOURS AT ROOM TEMPERATURE TO FORM THE ANTIBODY-ANTIGEN COMPLEX BEFORE MIXING WITH CRYSTALLISATION ...Details: PVAMA1 AND FAB-F8.12.19 WERE MIXED IN A 1:1 STOICHIOMETRIC RATIO AND LEFT TO INCUBATE FOR 4 HOURS AT ROOM TEMPERATURE TO FORM THE ANTIBODY-ANTIGEN COMPLEX BEFORE MIXING WITH CRYSTALLISATION SCREENING BUFFERS. CRYSTALS USED FOR DIFFRACTION MEASUREMENTS WERE OBTAINED AS FOLLOWS. THE CRYSTALLISATION BUFFER IN THE RESERVOIR COMPRISED 10% PEG 6000 AND 0.1 M SODIUM ACETATE BUFFERED TO PH 4.4. THE CRYSTALLISATION DROP WAS PREPARED BY ADDING 0.8 MICROLITRES OF THE CRYSTALLISATION BUFFER TO 0.8 MICROLITRES OF THE PVAMA1-FAB COMPLEX, GIVING A FINAL PROTEIN CONCENTRATION OF 3.9 MG/ML. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→20 Å / Num. obs: 26533 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.93 / % possible all: 88 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRIES 2IGF, 1W8K Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.612 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FAB LIGHT AND HEAVY CHAINS ARE NUMBERED ACCORDING TO THE KABAT CONVENTION. ANTIGEN RESIDUES D43 TO D420 AND RESIDUES D455 TO D487 ARE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FAB LIGHT AND HEAVY CHAINS ARE NUMBERED ACCORDING TO THE KABAT CONVENTION. ANTIGEN RESIDUES D43 TO D420 AND RESIDUES D455 TO D487 ARE DISSORDERED IN THE CRYSTAL 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: 42.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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