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Yorodumi- PDB-5dqd: Structure of S55-5 Fab in complex with lipid A carbohydrate backbone -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dqd | |||||||||
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Title | Structure of S55-5 Fab in complex with lipid A carbohydrate backbone | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Carbohydrate binding / Antibody | |||||||||
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 | 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 | 5dqd.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dqd.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dqd_validation.pdf.gz | 825.4 KB | Display | wwPDB validaton report |
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Full document | 5dqd_full_validation.pdf.gz | 828.8 KB | Display | |
Data in XML | 5dqd_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 5dqd_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/5dqd ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqd | HTTPS FTP |
-Related structure data
Related structure data | 5dqjC 4m93S 4odsS 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: 24087.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) | ||
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#2: Antibody | Mass: 23846.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) | ||
#3: Polysaccharide | 2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-1-O-phosphono- ...2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Chemical | #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: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.0M LICL, 0.1M CITRIC ACID, AND 20% (W/V) PEG 6000, PH 5.0, VAPOR DIFFUSION, HANGING DROP, |
-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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 2013 / Details: VERTICAL FOCUSING MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.938→25 Å / Num. obs: 36075 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.111 / Χ2: 1.065 / Net I/av σ(I): 15.831 / Net I/σ(I): 7.8 / Num. measured all: 204429 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 3.93 / Num. unique all: 3847 / Χ2: 1.048 / Rejects: 0 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M93, 4ODS Resolution: 1.94→24.09 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 76.17 Å2 / Biso mean: 23.08 Å2 / Biso min: 3.85 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→24.09 Å
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LS refinement shell | Resolution: 1.94→2.01 Å / Rfactor Rfree: 0.2215 / Rfactor Rwork: 0.172 |