+Open data
-Basic information
Entry | Database: PDB / ID: 3phq | ||||||
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Title | Crystal structure of S64-4 in complex with KDO | ||||||
Components |
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Keywords | CARBOHYDRATE-BINDING PROTEIN / antibody / Fab / IgG / carbohydrate | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Evans, D.W. / Evans, S.V. | ||||||
Citation | Journal: Glycobiology / Year: 2011 Title: Structural insights into parallel strategies for germline antibody recognition of lipopolysaccharide from Chlamydia. Authors: Evans, D.W. / Muller-Loennies, S. / Brooks, C.L. / 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 | 3phq.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3phq.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 3phq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3phq_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 3phq_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 3phq_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3phq_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/3phq ftp://data.pdbj.org/pub/pdb/validation_reports/ph/3phq | HTTPS FTP |
-Related 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: 23849.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
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#2: Antibody | Mass: 23788.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
#3: Sugar | ChemComp-KDO / |
#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: 2.44 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 289 K / Method: hanging drop / pH: 8.5 Details: Sodium citrate tribasic dihydrate, 2-propanol, PEG 4000, pH 8.5, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 1, 2009 / Details: OSMIC BLUE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.826 Å / Num. obs: 31620 / % possible obs: 98.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.47 / SU B: 4.886 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 32.243 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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