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Yorodumi- PDB-3qnz: Orthorhombic form of IgG1 Fab fragment (in complex with antigenic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qnz | ||||||
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Title | Orthorhombic form of IgG1 Fab fragment (in complex with antigenic tubulin peptide) sharing same Fv as IgA | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin fold | ||||||
Function / homology | Function and homology information odontoblast differentiation / cytoskeleton-dependent intracellular transport / natural killer cell mediated cytotoxicity / GTPase activating protein binding / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / microtubule-based process / spindle assembly ...odontoblast differentiation / cytoskeleton-dependent intracellular transport / natural killer cell mediated cytotoxicity / GTPase activating protein binding / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / microtubule-based process / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / structural constituent of cytoskeleton / mitotic spindle / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / mitotic cell cycle / cell body / microtubule / Potential therapeutics for SARS / cytoskeleton / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / GTP binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Trajtenberg, F. / Correa, A. / Buschiazzo, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure of a human IgA1 Fab fragment at 1.55 angstrom resolution: potential effect of the constant domains on antigen-affinity modulation Authors: Correa, A. / Trajtenberg, F. / Obal, G. / Pritsch, O. / Dighiero, G. / Oppezzo, P. / Buschiazzo, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qnz.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qnz.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qnz_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
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Full document | 3qnz_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | 3qnz_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 3qnz_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/3qnz ftp://data.pdbj.org/pub/pdb/validation_reports/qn/3qnz | HTTPS FTP |
-Related structure data
Related structure data | 3m8oC 3qnxC 3qnyC 3qo1C 3qo0S 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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-Components
#1: Antibody | Mass: 24009.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human) |
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#2: Antibody | Mass: 23200.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human) |
#3: Protein/peptide | Mass: 1155.079 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Standard peptide synthesis. The sequence occurs in several species, such as human, mouse, horse, rat, amphibians, etc. References: UniProt: P07437 |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.52 Å3/Da / Density % sol: 51.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Na citrate, 20% isopropanol, 16% PEG 4000, pH 5.5, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 108 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 14, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Varimax-HF 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: 2.2→68.84 Å / Num. all: 25641 / Num. obs: 25641 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 37.93 Å2 / Rsym value: 0.074 / Net I/σ(I): 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QO0 Resolution: 2.2→28.21 Å / Cor.coef. Fo:Fc: 0.9289 / Cor.coef. Fo:Fc free: 0.9004 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: TLS refinement was performed
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Displacement parameters | Biso max: 115.51 Å2 / Biso mean: 34.7038 Å2 / Biso min: 14.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.282 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→28.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.29 Å / Total num. of bins used: 13
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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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