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- PDB-5nqg: Crystal structure of Plasmodium vivax AMA1 in complex with a 39 a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nqg | ||||||
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Title | Crystal structure of Plasmodium vivax AMA1 in complex with a 39 aa PvRON2 peptide | ||||||
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![]() | CELL INVASION / AMA1 / RON2 / Malaria | ||||||
Function / homology | Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / membrane => GO:0016020 / membrane / Rhoptry neck protein 2 / Apical merozoite antigen 1 / Apical merozoite antigen 1![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vulliez-le Normand, B. / Saul, F.A. / Faber, B.W. / Bentley, G.A. | ||||||
![]() | ![]() Title: Cross-reactivity between apical membrane antgen 1 and rhoptry neck protein 2 in P. vivax and P. falciparum: A structural and binding study. Authors: Vulliez-Le Normand, B. / Saul, F.A. / Hoos, S. / Faber, B.W. / Bentley, G.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.1 KB | Display | ![]() |
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PDB format | ![]() | 77.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 438.9 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nqfC ![]() 1w8kS 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: 54413.008 Da / Num. of mol.: 1 / Mutation: Q119E, S178N, N226D, N441Q Source method: isolated from a genetically manipulated source Details: EXPRESSION TAG: E1, A2, S3, I4 ENGINEERED MUTATIONS : Q119E, S178N, N226D, N441Q. EXPRESSION TAG: LEQKLISEEDLNSAVDHHHHHH Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 4106.740 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() References: UniProt: A5K3N8 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 3350, sodium citrate, isopropanol |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→42.5 Å / Num. obs: 28667 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4162 / CC1/2: 0.698 / Rpim(I) all: 0.452 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1W8K Resolution: 2.15→39.58 Å / Cor.coef. Fo:Fc: 0.9233 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.197 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.174
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Displacement parameters | Biso mean: 49.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.297 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→39.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.23 Å / Total num. of bins used: 14
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