+Open data
-Basic information
Entry | Database: PDB / ID: 2ok0 | ||||||
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Title | Fab ED10-DNA complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM/DNA / immunoglobulin fold / IMMUNE SYSTEM-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Stanfield, R.L. / Sanguineti, S. / Wilson, I.A. / de Prat-Gay, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Specific recognition of a DNA immunogen by its elicited antibody Authors: Sanguineti, S. / Centeno Crowley, J.M. / Lodeiro Merlo, M.F. / Cerutti, M.L. / Wilson, I.A. / Goldbaum, F.A. / Stanfield, R.L. / de Prat-Gay, G. | ||||||
History |
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Remark 999 | SEQUENCE Currently, there is no aminoacid sequence database reference available for the proteins |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ok0.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ok0.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ok0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/2ok0 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/2ok0 | 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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Details | Chains L, H and D (one Fab-DNA complex) |
-Components
#1: DNA chain | Mass: 548.417 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Antibody | Mass: 24148.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3*PLUS |
#3: Antibody | Mass: 23491.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0N7J2*PLUS |
#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: 3.08 Å3/Da / Density % sol: 60.05 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 15% PEG 6000, 0.05M KCl, 0.01M MgCL2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.427 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→40.5 Å / Num. all: 44585 / Num. obs: 44585 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 4.6 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 2106 / Rsym value: 43.3 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→40.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 6.471 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.113 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→40.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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