+Open data
-Basic information
Entry | Database: PDB / ID: 5dqj | ||||||
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Title | Structure of unliganded S55-5 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / Fab / carbohydrate binding / Phospholipid | ||||||
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: 2.61 Å | ||||||
Authors | Haji-Ghassemi, O. / Evans, S.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Lipid A-antibody structures reveal a widely-utilized pocket specific for negatively charged groups derived from unrelated V-genes 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 | 5dqj.cif.gz | 177.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dqj.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 5dqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/5dqj ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqj | HTTPS FTP |
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-Related structure data
Related structure data | 5dqdSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Antibody | Mass: 24087.510 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 23846.869 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) #3: 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: 2.64 Å3/Da / Density % sol: 53.36 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 5% (w/v) glycerol and 15% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 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: Dec 1, 2011 / Details: Vertical focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→25 Å / Num. obs: 30002 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.037 / Rrim(I) all: 0.071 / Χ2: 0.909 / Net I/av σ(I): 18.743 / Net I/σ(I): 17 / Num. measured all: 111916 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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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: 5DQD Resolution: 2.61→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2414 / WRfactor Rwork: 0.1981 / FOM work R set: 0.8206 / SU B: 11.116 / SU ML: 0.232 / SU R Cruickshank DPI: 1.1244 / SU Rfree: 0.2959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.124 / ESU R Free: 0.296 / 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: 120 Å2 / Biso mean: 67.347 Å2 / Biso min: 31.72 Å2
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Refinement step | Cycle: final / Resolution: 2.61→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.606→2.673 Å / Total num. of bins used: 20
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