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Yorodumi- PDB-4z95: Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-5(d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z95 | |||||||||
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Title | Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-5(dT)-p-3' | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/DNA / antibody / Fab / carbohydrate / lipid A / DNA / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å | |||||||||
Authors | Haji-Ghassemi, O. / Evans, S.V. | |||||||||
Funding support | Canada, Austria, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural Basis for Antibody Recognition of Lipid A: INSIGHTS TO POLYSPECIFICITY TOWARD SINGLE-STRANDED DNA. Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Rodriguez, T. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z95.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z95.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 4z95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z95_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
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Full document | 4z95_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 4z95_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 4z95_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/4z95 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/4z95 | HTTPS FTP |
-Related structure data
Related structure data | 4odsC 4odtSC 4oduC 4odvC 4odwC 4z8fC 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 24436.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
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#2: Antibody | Mass: 23727.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Compound details | the ligand used for crystallization was 5'-DTpDTpDTpDTpDTp-3', however only a phosphate could be ...the ligand used for crystallization was 5'-DTpDTpDTpDTpDTp-3', however only a phosphate could be confidently modeled due to lack of electron density. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5, 25% (v/v) PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2014 / Details: Vertical focusing mirror |
Radiation | Monochromator: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→25 Å / Num. all: 457680 / Num. obs: 43749 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rsym value: 0.053 / Net I/σ(I): 37.7 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 10 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ODT Resolution: 1.79→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2437 / WRfactor Rwork: 0.2146 / FOM work R set: 0.7944 / SU B: 3.375 / SU ML: 0.103 / SU R Cruickshank DPI: 0.131 / SU Rfree: 0.1245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.124 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.19 Å2 / Biso mean: 38.743 Å2 / Biso min: 19.81 Å2
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Refinement step | Cycle: final / Resolution: 1.79→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.837 Å / Total num. of bins used: 20
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