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Yorodumi- PDB-4z0d: Crystal structure of FVO strain Plasmodium falciparum AMA1 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z0d | ||||||
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Title | Crystal structure of FVO strain Plasmodium falciparum AMA1 in complex with the RON2hp [Phe2038Trp] peptide | ||||||
Components |
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Keywords | CELL INVASION / inhibitor / AMA1 / malaria | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum Vietnam Oak-Knoll (eukaryote) Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Wang, G. / McGowan, S. / Norton, R.S. / Scanlon, M.J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Structure-Activity Studies of beta-Hairpin Peptide Inhibitors of the Plasmodium falciparum AMA1-RON2 Interaction. Authors: Wang, G. / Drinkwater, N. / Drew, D.R. / MacRaild, C.A. / Chalmers, D.K. / Mohanty, B. / Lim, S.S. / Anders, R.F. / Beeson, J.G. / Thompson, P.E. / McGowan, S. / Simpson, J.S. / Norton, R.S. / Scanlon, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z0d.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z0d.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 4z0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z0d_validation.pdf.gz | 430.2 KB | Display | wwPDB validaton report |
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Full document | 4z0d_full_validation.pdf.gz | 433 KB | Display | |
Data in XML | 4z0d_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 4z0d_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/4z0d ftp://data.pdbj.org/pub/pdb/validation_reports/z0/4z0d | 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: 38333.805 Da / Num. of mol.: 1 / Fragment: UNP residues 104-438 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum Vietnam Oak-Knoll (FVO) (eukaryote) Strain: FVO / Gene: PFFVO_05649 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A024UZE1 |
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#2: Protein/peptide | Mass: 1551.831 Da / Num. of mol.: 1 / Fragment: UNP residues 1217-1229 / Mutation: Phe2038Trp / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: Q8IKV6*PLUS |
#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 Å3/Da / Density % sol: 38.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 15-20% PEG400, 0.1 M Tris-HCl, pH 8.6, 0.1 M sodium acetate and 20% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9464 Å | |||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 7, 2014 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9464 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.1→38.53 Å / Num. obs: 19242 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.32 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.313 / Rpim(I) all: 0.128 / Net I/σ(I): 5.4 / Num. measured all: 133011 / Scaling rejects: 104 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 2.1→36.058 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.43 Å2 / Biso mean: 25.1716 Å2 / Biso min: 6.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→36.058 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -8.6144 Å / Origin y: 2.8462 Å / Origin z: -7.3553 Å
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Refinement TLS group |
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