+Open data
-Basic information
Entry | Database: PDB / ID: 4r1a | ||||||
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Title | Crystal Structure of FVO strain Plasmodium falciparum AMA1 | ||||||
Components | Apical membrane antigen 1 | ||||||
Keywords | CELL INVASION / PAN fold / erythrocyte invasion by merozoites / RON2 / Moving junction complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum FCR-3/Gambia (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lim, S.S. / Norton, R.S. / McGowan, S. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structure and Dynamics of Apical Membrane Antigen 1 from Plasmodium falciparum FVO. Authors: Lim, S.S. / Yang, W. / Krishnarjuna, B. / Kannan Sivaraman, K. / Chandrashekaran, I.R. / Kass, I. / MacRaild, C.A. / Devine, S.M. / Debono, C.O. / Anders, R.F. / Scanlon, M.J. / Scammells, P. ...Authors: Lim, S.S. / Yang, W. / Krishnarjuna, B. / Kannan Sivaraman, K. / Chandrashekaran, I.R. / Kass, I. / MacRaild, C.A. / Devine, S.M. / Debono, C.O. / Anders, R.F. / Scanlon, M.J. / Scammells, P.J. / Norton, R.S. / McGowan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r1a.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r1a.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 4r1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/4r1a ftp://data.pdbj.org/pub/pdb/validation_reports/r1/4r1a | HTTPS FTP |
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-Related structure data
Related structure data | 4r19C 4r1bC 4r1cC 1z40S 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: 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 FCR-3/Gambia (eukaryote) Strain: isolate FCR-3 / Gambia / Gene: AMA-1, PF83 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P50490 |
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#2: 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: 1.94 Å3/Da / Density % sol: 36.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25.0% (v/v) PEG 3350, 0.1 M HEPES, 0.2 M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2014 |
Radiation | Monochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2→35.72 Å / Num. obs: 19576 / % possible obs: 97.5 % / Observed criterion σ(I): 8 / Biso Wilson estimate: 21.8 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Z40 Resolution: 2→35.72 Å / SU ML: 0.27 / σ(F): 1.33 / Phase error: 30.64 / 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→35.72 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: -22.3982 Å / Origin y: 2.2987 Å / Origin z: 16.6863 Å
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Refinement TLS group | Selection details: all |