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Yorodumi- PDB-4bh7: CRYSTAL STRUCTURE OF GERMLINE ANTIBODY 36-65 IN COMPLEX WITH PEPT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bh7 | ||||||
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Title | CRYSTAL STRUCTURE OF GERMLINE ANTIBODY 36-65 IN COMPLEX WITH PEPTIDE PPYPAWHAPGNI | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CONVERGENCE OF ANTIBODY SPECIFICITIES | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Khan, T. / Salunke, D.M. | ||||||
Citation | Journal: J.Immunol. / Year: 2014 Title: Adjustable Locks and Flexible Keys: Plasticity of Epitope-Paratope Interactions in Germline Antibodies. Authors: Khan, T. / Salunke, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bh7.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bh7.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 4bh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/4bh7 ftp://data.pdbj.org/pub/pdb/validation_reports/bh/4bh7 | HTTPS FTP |
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-Related structure data
Related structure data | 4bh8C 2a6jS 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
#1: Antibody | Mass: 23620.893 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B CELL / Cell line: 36-65 HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C |
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#2: Antibody | Mass: 23942.768 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B CELL / Cell line: 36-65 HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C |
#3: Protein/peptide | Mass: 1320.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#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: 2.4 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.05 M SODIUM CACODYLATE PH 6.5, 18% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 13, 2006 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER CMF12 38CU-6 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→57 Å / Num. obs: 10548 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.89→3.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A6J Resolution: 2.89→57.81 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 15.702 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.325 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.643 Å2
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Refinement step | Cycle: LAST / Resolution: 2.89→57.81 Å
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Refine LS restraints |
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