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Yorodumi- PDB-3e8u: Crystal structure and thermodynamic analysis of diagnostic Fab 10... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e8u | ||||||
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Title | Crystal structure and thermodynamic analysis of diagnostic Fab 106.3 complexed with BNP 5-13 (C10A) reveal basis of selective molecular recognition | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab 106.3 / IgG1 / Brain Natriuretic Peptide (BNP) | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Longenecker, K.L. / Ruan, Q. / Fry, E.H. / Saldana, S.S. / Brophy, S.E. / Richardson, P.L. / Tetin, S.Y. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Crystal structure and thermodynamic analysis of diagnostic mAb 106.3 complexed with BNP 5-13 (C10A). Authors: Longenecker, K.L. / Ruan, Q. / Fry, E.H. / Saldana, S.C. / Brophy, S.E. / Richardson, P.L. / Tetin, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e8u.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e8u.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e8u_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 3e8u_full_validation.pdf.gz | 434.1 KB | Display | |
Data in XML | 3e8u_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3e8u_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/3e8u ftp://data.pdbj.org/pub/pdb/validation_reports/e8/3e8u | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23394.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23761.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
#3: Protein/peptide | Mass: 993.057 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#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: 2.49 Å3/Da / Density % sol: 50.59 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 25672 / % possible obs: 90.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.089 / Χ2: 1.055 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.1→44.73 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.835 / SU B: 5.039 / SU ML: 0.134 / SU R Cruickshank DPI: 0.263 / SU Rfree: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.213 / 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 max: 47.51 Å2 / Biso mean: 20.195 Å2 / Biso min: 5.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→44.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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