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Yorodumi- PDB-3sri: Crystal structure of Plasmodium falciparum AMA1 in complex with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sri | ||||||
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Title | Crystal structure of Plasmodium falciparum AMA1 in complex with a 29aa PfRON2 peptide | ||||||
Components |
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Keywords | CELL INVASION / AMA1 / Plasmodium falciparum / RON2 / malaria | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Vulliez-Le Normand, B. / Saul, F.A. / Bentley, G.A. | ||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: Structural and functional insights into the malaria parasite moving junction complex. Authors: Vulliez-Le Normand, B. / Tonkin, M.L. / Lamarque, M.H. / Langer, S. / Hoos, S. / Roques, M. / Saul, F.A. / Faber, B.W. / Bentley, G.A. / Boulanger, M.J. / Lebrun, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sri.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sri.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 3sri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/3sri ftp://data.pdbj.org/pub/pdb/validation_reports/sr/3sri | HTTPS FTP |
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-Related structure data
Related structure data | 3srjC 3zwzC 1z40S 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: 43664.867 Da / Num. of mol.: 1 / Fragment: AMA1 / Mutation: N162K, T288V, S373D, N422D, S423K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: CAMP/Malaysia / Gene: AMA-1, PF83 / Production host: Pichia pastoris (fungus) / References: UniProt: P50489 |
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#2: Protein/peptide | Mass: 3036.505 Da / Num. of mol.: 1 / Fragment: RON2 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: Q8IKV6 |
#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: 2.06 Å3/Da / Density % sol: 40.36 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 20% PEG 4000, 0.1M Tris/HCL, 0.1M sodium acetate, 20% isopropanol, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95367 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95367 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.97 Å / Num. all: 48207 / Num. obs: 48207 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 22.19 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6821 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Z40 Resolution: 1.6→35.04 Å / Cor.coef. Fo:Fc: 0.9517 / Cor.coef. Fo:Fc free: 0.9475 / SU R Cruickshank DPI: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.98 Å2
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→35.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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