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Open data
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Basic information
Entry | Database: PDB / ID: 2z8v | ||||||
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Title | Structure of an IgNAR-AMA1 complex | ||||||
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![]() | IMMUNE SYSTEM / AMA1-VNAR complex / 14I-1 / Receptor | ||||||
Function / homology | ![]() apical complex / microneme / host cell surface binding / symbiont entry into host / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Streltsov, V.A. / Henderson, K.A. / Batchelor, A.H. / Coley, A.M. / Nuttall, S.D. | ||||||
![]() | ![]() Title: Structure of an IgNAR-AMA1 Complex: Targeting a Conserved Hydrophobic Cleft Broadens Malarial Strain Recognition Authors: Henderson, K.A. / Streltsov, V.A. / Coley, A.M. / Dolezal, O. / Hudson, P.J. / Batchelor, A.H. / Gupta, A. / Bai, T. / Murphy, V.J. / Anders, R.F. / Foley, M. / Nuttall, S.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.2 KB | Display | ![]() |
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PDB format | ![]() | 157.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.8 KB | Display | ![]() |
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Full document | ![]() | 487.1 KB | Display | |
Data in XML | ![]() | 41.1 KB | Display | |
Data in CIF | ![]() | 58.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2z8wC ![]() 1verS ![]() 1z40S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38360.047 Da / Num. of mol.: 2 / Fragment: domain I, II, UNP residues 104-438 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Plasmid: pPROEXHTB / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Protein | Mass: 12811.331 Da / Num. of mol.: 2 / Mutation: F29L/G92R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pGC / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.1M phosphate citrate pH 4.2, 0.2M NaCl, 15% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→66.08 Å / Num. all: 34389 / Num. obs: 34389 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1Z40 and 1VER Resolution: 2.35→38.19 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.906 / SU B: 23.513 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.71 / ESU R Free: 0.327 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.687 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→38.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.347→2.408 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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