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Yorodumi- PDB-3s62: Structure of Fab fragment of malaria transmission blocking antibo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s62 | ||||||
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Title | Structure of Fab fragment of malaria transmission blocking antibody 2A8 against P. vivax P25 protein | ||||||
Components |
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Keywords | IMMUNE SYSTEM / typical antibody fold | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.01 Å | ||||||
Authors | Saxena, A.K. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2012 Title: Structure of Fab fragment of malaria transmission blocking antibody 2A8 against P. vivax P25 protein Authors: Saxena, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s62.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s62.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 3s62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/3s62 ftp://data.pdbj.org/pub/pdb/validation_reports/s6/3s62 | HTTPS FTP |
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-Related structure data
Related structure data | 1z3gS S: Starting model for refinement |
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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: Antibody | Mass: 23282.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: Ascites fluid |
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#2: Antibody | Mass: 23113.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: Ascites fluid |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.79 Å3/Da / Density % sol: 74.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, 25% PEGMME550, 10mM ZnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 14, 2004 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4→100 Å / Num. all: 7804 / Num. obs: 7444 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.15 / Net I/σ(I): 13.2 |
Reflection shell | Highest resolution: 4.009 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 13.2 / Num. unique all: 7444 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z3G Resolution: 4.01→50 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.87 / SU B: 55.388 / SU ML: 0.73 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.834 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 100.907 Å2
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Refinement step | Cycle: LAST / Resolution: 4.01→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.009→4.113 Å / Total num. of bins used: 20
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