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Yorodumi- PDB-4dcq: Crystal Structure of the Fab Fragment of 3B5H10, an Antibody-Spec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dcq | ||||||
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Title | Crystal Structure of the Fab Fragment of 3B5H10, an Antibody-Specific for Extended Polyglutamine Repeats (orthorhombic form) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab fragment / immunoglobulin domain / anti-polyglutamine / polyglutamine repeats | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | ||||||
Authors | Peters-Libeu, C.A. / Tran, T. / Finkbeiner, S. / Weisgraber, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Disease-associated polyglutamine stretches in monomeric huntingtin adopt a compact structure. Authors: Peters-Libeu, C. / Miller, J. / Rutenber, E. / Newhouse, Y. / Krishnan, P. / Cheung, K. / Hatters, D. / Brooks, E. / Widjaja, K. / Tran, T. / Mitra, S. / Arrasate, M. / Mosquera, L.A. / ...Authors: Peters-Libeu, C. / Miller, J. / Rutenber, E. / Newhouse, Y. / Krishnan, P. / Cheung, K. / Hatters, D. / Brooks, E. / Widjaja, K. / Tran, T. / Mitra, S. / Arrasate, M. / Mosquera, L.A. / Taylor, D. / Weisgraber, K.H. / Finkbeiner, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dcq.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dcq.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 4dcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dcq_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 4dcq_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 4dcq_validation.xml.gz | 23 KB | Display | |
Data in CIF | 4dcq_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/4dcq ftp://data.pdbj.org/pub/pdb/validation_reports/dc/4dcq | HTTPS FTP |
-Related structure data
Related structure data | 3s96SC 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 23611.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: monoclonal antibody / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA | ||
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#2: Antibody | Mass: 23487.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: monoclonal antibody / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA | ||
#3: Chemical | #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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG 3350, 200 mM citric acid,0.7% ethylene glycol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 78 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→30 Å / Num. all: 32012 / Num. obs: 29497 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.071 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1525 / Rsym value: 0.27 / % possible all: 74.26 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 46.2 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S96 Resolution: 1.94→11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2418 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8356 / SU B: 4.089 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1994 / SU Rfree: 0.1801 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 73.13 Å2 / Biso mean: 25.4097 Å2 / Biso min: 8.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.989 Å / Total num. of bins used: 20
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