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Yorodumi- PDB-8gid: Crystal structure of a strain-transcending single-component Plasm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gid | ||||||
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Title | Crystal structure of a strain-transcending single-component Plasmodium falciparum AMA1-RON2L structure-based design immunogen 1 (SBD1) | ||||||
Components | Apical membrane antigen 1, rhoptry neck protein 2 chimera | ||||||
Keywords | CELL INVASION / Single component immunogens / Malaria vaccines | ||||||
Function / homology | Function and homology information rhoptry neck / apical complex / microneme / host cell surface binding / symbiont entry into host / membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Patel, P.N. / Tolia, N.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure-based design of a strain transcending AMA1-RON2L malaria vaccine. Authors: Patel, P.N. / Dickey, T.H. / Diouf, A. / Salinas, N.D. / McAleese, H. / Ouahes, T. / Long, C.A. / Miura, K. / Lambert, L.E. / Tolia, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gid.cif.gz | 253.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gid.ent.gz | 169.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gid_validation.pdf.gz | 430.3 KB | Display | wwPDB validaton report |
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Full document | 8gid_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 8gid_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 8gid_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/8gid ftp://data.pdbj.org/pub/pdb/validation_reports/gi/8gid | HTTPS FTP |
-Related structure data
Related structure data | 8gieC 8gifC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41729.453 Da / Num. of mol.: 1 / Mutation: T137A,T261A,S41A,S42A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: ama1, PF3D7_1133400, PF3D7_1452000 / Plasmid: pHL-sec / Cell (production host): 293 derived Cells / Cell line (production host): Expi293F / Production host: Homo sapiens (human) References: UniProt: D9MXR5, UniProt: Q7KQK5, UniProt: Q8IKV6 |
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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: 2.36 Å3/Da / Density % sol: 47.81 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium sulfate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.81 Å / Num. obs: 32748 / % possible obs: 97.05 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0701 / Rpim(I) all: 0.0447 / Rrim(I) all: 0.0834 / Net I/σ(I): 12.22 |
Reflection shell | Resolution: 1.8→1.864 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7521 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 3112 / CC1/2: 0.663 / CC star: 0.893 / Rpim(I) all: 0.4763 / Rrim(I) all: 0.8935 / % possible all: 96.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.81 Å / SU ML: 0.2176 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1616 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.81 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: 20.0874617637 Å / Origin y: 1.07071813671 Å / Origin z: 19.411366733 Å
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Refinement TLS group | Selection details: all |