+Open data
-Basic information
Entry | Database: PDB / ID: 2iqa | ||||||
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Title | PFA2 FAB fragment, monoclinic apo form | ||||||
Components | (IgG2a Fab fragment PFA2 ...) x 2 | ||||||
Keywords | IMMUNE SYSTEM / pfa2 / wwddd / cdr | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / 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 | 2iqa.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iqa.ent.gz | 145 KB | Display | PDB format |
PDBx/mmJSON format | 2iqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/2iqa ftp://data.pdbj.org/pub/pdb/validation_reports/iq/2iqa | HTTPS FTP |
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-Related structure data
Related structure data | 2iptC 2ipuC 2iq9SC 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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2 |
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Unit cell |
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Details | The biological assembly is a heterodimer. |
-Components
-Antibody , 2 types, 4 molecules LAHB
#1: Antibody | Mass: 24146.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: A2NHM3 #2: Antibody | Mass: 23903.994 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: Q811U5 |
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-Non-polymers , 4 types, 283 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: 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: 2.74 Å3/Da / Density % sol: 55.14 % |
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Crystal grow | Method: vapor diffusion / pH: 6.5 Details: 0.1 M Bis-Tris, 28% PEG-MME 2000, pH 6.5, VAPOR DIFFUSION |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2005 | |||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2→33.45 Å / Num. obs: 70368 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.09 / Net I/σ(I): 22.3 | |||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.26 / Num. unique all: 6934 / Rsym value: 0.405 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IQ9 Resolution: 2→33.45 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.731 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.185 / 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: 35.142 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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