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Yorodumi- PDB-2q8a: Structure of the malaria antigen AMA1 in complex with a growth-in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q8a | ||||||
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Title | Structure of the malaria antigen AMA1 in complex with a growth-inhibitory antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antigen-antibody complex | ||||||
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) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Gupta, A. / Murphy, V.J. / Anders, R.F. / Batchelor, A.H. | ||||||
Citation | Journal: PLoS Pathog. / Year: 2007 Title: Structure of the malaria antigen AMA1 in complex with a growth-inhibitory antibody. Authors: Coley, A.M. / Gupta, A. / Murphy, V.J. / Bai, T. / Kim, H. / Foley, M. / Anders, R.F. / Batchelor, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q8a.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q8a.ent.gz | 120.2 KB | Display | PDB format |
PDBx/mmJSON format | 2q8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q8a_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 2q8a_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 2q8a_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 2q8a_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/2q8a ftp://data.pdbj.org/pub/pdb/validation_reports/q8/2q8a | HTTPS FTP |
-Related structure data
Related structure data | 2q8bC 1z40S 2cgrS 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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Unit cell |
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-Components
#1: Protein | Mass: 38417.102 Da / Num. of mol.: 1 / Fragment: Domains I and II (RESIDUES 104-438) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: AMA1 / Plasmid: pPROEXHTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7KQK5 |
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#2: Antibody | Mass: 23698.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Hybridoma cell line / Source: (natural) Mus musculus (house mouse) |
#3: Antibody | Mass: 22345.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Hybridoma cell line / Source: (natural) Mus musculus (house mouse) |
#4: 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: 2.45 Å3/Da / Density % sol: 49.89 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20 MM MES, 10 MM MNCL2, 6 % PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: osmic multilayer |
Radiation | Monochromator: Osmic multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 30851 / Num. obs: 30851 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.061 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.23 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z40, 2CGR Resolution: 2.4→38.92 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.426 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.428 / ESU R Free: 0.259 / 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: 35.073 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→38.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 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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