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Yorodumi- PDB-2rji: Malarial EBA-175 region VI crystallographic structure reveals a K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rji | ||||||
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Title | Malarial EBA-175 region VI crystallographic structure reveals a KIX-like binding interface | ||||||
Components | Erythrocyte binding antigen 175 | ||||||
Keywords | PROTEIN TRANSPORT / CELL INVASION / CBP KIX / EBA-175 / Plasmodium falciparum / region VI | ||||||
Function / homology | Function and homology information : / membrane => GO:0016020 / host cell surface receptor binding / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Withers-Martinez, C. / Blackman, M.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Malarial EBA-175 Region VI Crystallographic Structure Reveals a KIX-Like Binding Interface Authors: Withers-Martinez, C. / Haire, L.F. / Hackett, F. / Walker, P.A. / Howell, S.A. / Smerdon, S.J. / Dodson, G.G. / Blackman, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rji.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rji.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 2rji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/2rji ftp://data.pdbj.org/pub/pdb/validation_reports/rj/2rji | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10010.240 Da / Num. of mol.: 2 / Fragment: UNP residues 1307-1389 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: eba175reVIsynth / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q9NG63, UniProt: Q25842*PLUS #2: Chemical | ChemComp-CA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M citric acid, 1M LiCl, 25-30% PEG 6K, pH4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.8→30 Å / Num. obs: 16406 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.3 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2030 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→27.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.549 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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