+Open data
-Basic information
Entry | Database: PDB / ID: 4nj9 | ||||||
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Title | Crystal structure of Fab 8B10 in complex with MPTS | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin fold / MPTS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Stanfield, R.L. / Romesberg, F.E. / Zimmermann, J. / Wilson, I.A. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation. Authors: Adhikary, R. / Yu, W. / Oda, M. / Walker, R.C. / Chen, T. / Stanfield, R.L. / Wilson, I.A. / Zimmermann, J. / Romesberg, F.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nj9.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nj9.ent.gz | 151.1 KB | Display | PDB format |
PDBx/mmJSON format | 4nj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/4nj9 ftp://data.pdbj.org/pub/pdb/validation_reports/nj/4nj9 | 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: 24030.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma cells / Source: (natural) Mus musculus (house mouse) / Strain: swiss webster / References: UniProt: Q52L95, UniProt: Q7TS98*PLUS | ||||
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#2: Antibody | Mass: 24572.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma cells / Source: (natural) Mus musculus (house mouse) / Strain: swiss webster / References: UniProt: Q9D8L4 | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-2M9 / | #5: 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: 49.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2M zinc acetate, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03318 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→32.9 Å / Num. all: 35255 / Num. obs: 35255 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→32.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.865 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. LARGE UNACCOUNTED FOR ELECTRON DENSITY PRESENT NEAR (-9.427, 14.785, 50.439). There are several strong positive electron density features ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. LARGE UNACCOUNTED FOR ELECTRON DENSITY PRESENT NEAR (-9.427, 14.785, 50.439). There are several strong positive electron density features that the authors were unable to identify. These are close to side chains L55, H181 and H214.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.895 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→32.9 Å
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Refine LS restraints |
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