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Yorodumi- PDB-6n87: Plasmodium falciparum FVO apical membrane antigen 1 (AMA1) bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n87 | ||||||
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Title | Plasmodium falciparum FVO apical membrane antigen 1 (AMA1) bound to MTSL spin-labelled cyclised RON2 peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / AMA1 / apical membrane antigen 1 / malaria / RON2 / paramagnetic probe | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.588 Å | ||||||
Authors | McGowan, S. / Drinkwater, N. | ||||||
Funding support | Australia, 1items
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Citation | Journal: ChemMedChem / Year: 2019 Title: Identification of the Binding Site of Apical Membrane Antigen 1 (AMA1) Inhibitors Using a Paramagnetic Probe. Authors: Akter, M. / Drinkwater, N. / Devine, S.M. / Drew, S.C. / Krishnarjuna, B. / Debono, C.O. / Wang, G. / Scanlon, M.J. / Scammells, P.J. / McGowan, S. / MacRaild, C.A. / Norton, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n87.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n87.ent.gz | 123.6 KB | Display | PDB format |
PDBx/mmJSON format | 6n87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n87_validation.pdf.gz | 779.6 KB | Display | wwPDB validaton report |
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Full document | 6n87_full_validation.pdf.gz | 783.2 KB | Display | |
Data in XML | 6n87_validation.xml.gz | 18 KB | Display | |
Data in CIF | 6n87_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/6n87 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/6n87 | HTTPS FTP |
-Related structure data
Related structure data | 6n7qC 4r1aS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 38390.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: ama-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): DI+DII / References: UniProt: Q1PBJ5 |
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#2: Protein/peptide | Mass: 1548.870 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) |
#3: Chemical | ChemComp-MTN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 15-20% PEG400, 0.1 M Tris pH 8.4, 20% isopropanol, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.588→40.79 Å / Num. obs: 51482 / % possible obs: 99.57 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rpim(I) all: 0.056 / Net I/σ(I): 8.62 |
Reflection shell | Resolution: 1.588→1.644 Å / Num. unique obs: 4902 / CC1/2: 0.493 / Rpim(I) all: 0.569 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R1A Resolution: 1.588→40.787 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.588→40.787 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 71.3163 Å / Origin y: 8.0583 Å / Origin z: 25.549 Å
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Refinement TLS group | Selection details: all |