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Yorodumi- PDB-4bh8: CRYSTAL STRUCTURE OF GERMLINE ANTIBODY 36-65 IN COMPLEX WITH PEPT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bh8 | ||||||
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Title | CRYSTAL STRUCTURE OF GERMLINE ANTIBODY 36-65 IN COMPLEX WITH PEPTIDE GDPRPSYISHLL | ||||||
Components |
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Keywords | IMMUNE SYSTEM / GERMLINE ANTIBODY / ANTIBODY POLYSPECIFICTY | ||||||
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: 2.4 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 | 4bh8.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bh8.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/4bh8 ftp://data.pdbj.org/pub/pdb/validation_reports/bh/4bh8 | HTTPS FTP |
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-Related structure data
Related structure data | 4bh7C 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: 23663.084 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: 1356.528 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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NO |
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Crystal grow | pH: 6.7 / Details: 0.05 M SODIUM CACODYLATE, PH 6.7, 21% PEG |
-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: Apr 9, 2009 / 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: 2.4→58 Å / Num. obs: 19076 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A6J Resolution: 2.4→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.262 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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