[English] 日本語
Yorodumi- PDB-8gif: Crystal structure of a designed single-component Plasmodium falci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gif | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a designed single-component Plasmodium falciparum AMA1-RON2L insertion fusion immunogen 3 | ||||||
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: 2.1 Å | ||||||
Authors | Patel, P.N. / Tolia, N.H. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gif.cif.gz | 231.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gif.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 8gif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/8gif ftp://data.pdbj.org/pub/pdb/validation_reports/gi/8gif | HTTPS FTP |
---|
-Related structure data
Related structure data | 8gidC 8gieC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39392.902 Da / Num. of mol.: 1 / Mutation: T64A,T233A,S333A,S334A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: 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: Q7KQK5, UniProt: Q8IKV6 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 36.03 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium chloride, 0.1 M Tris (pH 8.5), 20 % (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.71 Å / Num. obs: 17236 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 27.93 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.0686 / Rpim(I) all: 0.0445 / Rrim(I) all: 0.082 / Net I/σ(I): 12.07 |
Reflection shell | Resolution: 2.101→2.176 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.1663 / Mean I/σ(I) obs: 5.41 / Num. unique obs: 1600 / CC1/2: 0.953 / CC star: 0.988 / Rpim(I) all: 0.113 / Rrim(I) all: 0.2019 / % possible all: 92.38 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.71 Å / SU ML: 0.2234 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 21.3225 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.71 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 11.3207581173 Å / Origin y: 10.413349248 Å / Origin z: 5.03661866507 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |