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Yorodumi- PDB-6n7q: Plasmodium falciparum FVO apical membrane antigen 1 (AMA1) bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n7q | ||||||
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Title | Plasmodium falciparum FVO apical membrane antigen 1 (AMA1) bound to cyclised RON2 peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / AMA1 / apical membrane antigen 1 / malaria / RON2 / paramagnetic probe | ||||||
Function / homology | Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / membrane => GO:0016020 / Alpha Beta / Apical membrane antigen-1 Function and homology information | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 6n7q.cif.gz | 132.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n7q.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 6n7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n7q_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 6n7q_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 6n7q_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6n7q_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/6n7q ftp://data.pdbj.org/pub/pdb/validation_reports/n7/6n7q | HTTPS FTP |
-Related structure data
Related structure data | 6n87C 4r1aS S: Starting model for refinement C: citing same article (ref.) |
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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: 38391.840 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) / 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: 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: 2.1 Å3/Da / Density % sol: 41.36 % |
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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: 2.1→36.273 Å / Num. obs: 19742 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 5.75 |
Reflection shell | Resolution: 2.1→2.175 Å / Num. unique obs: 5980 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R1A Resolution: 2.1→36.273 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→36.273 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: 144.5045 Å / Origin y: -6.4144 Å / Origin z: 92.8503 Å
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Refinement TLS group | Selection details: all |