+Open data
-Basic information
Entry | Database: PDB / ID: 4hxa | ||||||
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Title | Crystal structure of 13D9 FAB | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIBODY / FAB / CARBOHYDRATE / COMPLEMENTARITY DETERMINING REGIONS | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Johal, A.R. / Jarrell, H.C. / Khieu, N.H. / Letts, J.A. / Landry, R.C. / Jachymek, W. / Yang, Q. / Jennings, H.J. / Brisson, J.R. / Evans, S.V. | ||||||
Citation | Journal: Glycobiology / Year: 2013 Title: The antigen-binding site of an N-propionylated polysialic acid-specific antibody protective against group B meningococci is consistent with extended epitopes. Authors: Johal, A.R. / Jarrell, H.C. / Letts, J.A. / Khieu, N.H. / Landry, R.C. / Jachymek, W. / Yang, Q. / Jennings, H.J. / Brisson, J.R. / 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 | 4hxa.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hxa.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/4hxa ftp://data.pdbj.org/pub/pdb/validation_reports/hx/4hxa | HTTPS FTP |
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-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: 23280.652 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: 23963.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ASCITES / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C |
#3: 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: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 10000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 19, 2006 / Details: OSMIC BLUE MIRRORS |
Radiation | Monochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→20 Å / Num. obs: 31114 / % possible obs: 88.4 % / Redundancy: 4.67 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 4.39 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.8 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FAB FROM YST9.1 Resolution: 2.06→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.884 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.221 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.11 Å / Total num. of bins used: 20
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