+Open data
-Basic information
Entry | Database: PDB / ID: 2z8w | ||||||
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Title | Structure of an IgNAR-AMA1 complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / AMA1-VNAR complex / 14I1-M15 / Receptor | ||||||
Function / homology | Function and homology information apical complex / microneme / host cell surface binding / symbiont entry into host / membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Orectolobus maculatus (spotted wobbegong) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Streltsov, V.A. / Henderson, K.A. / Batchelor, A.H. / Coley, A.M. / Nuttall, S.D. | ||||||
Citation | Journal: Structure / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z8w.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z8w.ent.gz | 157.2 KB | Display | PDB format |
PDBx/mmJSON format | 2z8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z8w_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 2z8w_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 2z8w_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 2z8w_validation.cif.gz | 56.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/2z8w ftp://data.pdbj.org/pub/pdb/validation_reports/z8/2z8w | HTTPS FTP |
-Related structure data
Related structure data | 2z8vC 1verS 1z40S S: Starting model for refinement C: citing same article (ref.) |
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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
#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.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: pPROEXHTB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7KQK5 #2: Protein | Mass: 12861.390 Da / Num. of mol.: 2 / Mutation: P90L/G92R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong) Plasmid: pGC / Production host: Escherichia coli (E. coli) / References: UniProt: Q6X1E6 #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: 2.32 Å3/Da / Density % sol: 47.07 % |
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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, 20% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.96426 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96426 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→66.23 Å / Num. all: 28622 / Num. obs: 28622 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.45→2.51 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1Z40 and 1VER Resolution: 2.45→38.33 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.865 / SU B: 23.776 / SU ML: 0.289 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.379 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.778 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→38.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.514 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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