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Yorodumi- PDB-5nqf: Crystal structure of Plasmodium falciparum AMA1 in complex with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nqf | ||||||
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Title | Crystal structure of Plasmodium falciparum AMA1 in complex with a 39 aa PvRON2 peptide | ||||||
Components |
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Keywords | CELL INVASION / AMA1 / RON2 / MALARIA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum Vietnam Oak-Knoll (eukaryote) Plasmodium vivax Sal-1 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Vulliez-le Normand, B. / Saul, F.A. / Faber, B.W. / Bentley, G.A. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nqf.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nqf.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nqf_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 5nqf_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 5nqf_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 5nqf_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/5nqf ftp://data.pdbj.org/pub/pdb/validation_reports/nq/5nqf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42690.598 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 97-442 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUES I97-P442 OF PFAMA1-FVO. N-TERMINAL STRETCH EF IS A CLONING ARTEFACT. C-TERMINAL STRETCH GLEQKLISEEDLNSAVDHHHHHH IS AN EXPRESSION TAG ( C-MYC + HEXA-HIS ). N162K, T288V, S373D, ...Details: RESIDUES I97-P442 OF PFAMA1-FVO. N-TERMINAL STRETCH EF IS A CLONING ARTEFACT. C-TERMINAL STRETCH GLEQKLISEEDLNSAVDHHHHHH IS AN EXPRESSION TAG ( C-MYC + HEXA-HIS ). N162K, T288V, S373D, N422D, S423K ARE ENGINEERED MUTATIONS. Source: (gene. exp.) Plasmodium falciparum Vietnam Oak-Knoll (FVO) (eukaryote) Gene: PFFVO_05649 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A024UZE1 |
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#2: Protein/peptide | Mass: 4106.740 Da / Num. of mol.: 1 / Fragment: UNP Residues 2034-2072 / Source method: obtained synthetically / Source: (synth.) Plasmodium vivax Sal-1 (eukaryote) / References: UniProt: A5K3N8 |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: PEG 3350, TRIS 8.2, SODIUM ACETATE, ISOPROPANOL, PH 8.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K PH range: 8.2 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91165 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2013 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91165 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.92 Å / Num. obs: 29741 / % possible obs: 96.2 % / Redundancy: 3 % / Biso Wilson estimate: 23.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.822 / % possible all: 78.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AMA1-FVO Resolution: 1.9→35.78 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.124
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Displacement parameters | Biso mean: 28.57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.214 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→35.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 15
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