+Open data
-Basic information
Entry | Database: PDB / ID: 2ipt | ||||||
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Title | PFA1 Fab Fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / wwddd / cdr / abeta | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gardberg, A.S. / Dealwis, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Molecular basis for passive immunotherapy of Alzheimer's disease Authors: Gardberg, A.S. / Dice, L.T. / Ou, S. / Rich, R.L. / Helmbrecht, E. / Ko, J. / Wetzel, R. / Myszka, D.G. / Patterson, P.H. / Dealwis, C. | ||||||
History |
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Remark 999 | SEQUENCE Presently, there is no aminoacid sequence database reference available for the two ...SEQUENCE Presently, there is no aminoacid sequence database reference available for the two proteins IGG2A FAB fragment heavy chain and IGG2A FAB fragment light chain kappa |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ipt.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ipt.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ipt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/2ipt ftp://data.pdbj.org/pub/pdb/validation_reports/ip/2ipt | HTTPS FTP |
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-Related structure data
Related structure data | 2ipuC 2iq9SC 2iqaC 2r0wC 2r0zC 2iqb C: citing same article (ref.) 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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Details | The biological assembly is a heterodimer. |
-Components
#1: Antibody | Mass: 24146.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: A2NHM3 |
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#2: Antibody | Mass: 23811.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: Q6PIP8 |
#3: Chemical | ChemComp-ACM / |
#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: 2.17 Å3/Da / Density % sol: 43.23 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M Hepes, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 27, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→25.19 Å / Num. obs: 25317 / % possible obs: 93.1 % / Redundancy: 1.9 % / Rsym value: 0.052 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.9 % / Rsym value: 0.186 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IQ9 Resolution: 2→25.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.345 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.181 / 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: 16.546 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.054 Å / Total num. of bins used: 20
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