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Yorodumi- PDB-2gki: Heavy and light chain variable single domains of an anti-DNA bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gki | ||||||
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Title | Heavy and light chain variable single domains of an anti-DNA binding antibody hydrolyze both double- and single-stranded DNAs without sequence specificity | ||||||
Components | nuclease | ||||||
Keywords | IMMUNE SYSTEM / anti-DNA antibody / catalytic antibody | ||||||
Function / homology | Function and homology information Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||
Authors | Kim, Y.R. / Kim, J.S. / Lee, S.H. / Lee, W.R. / Sohn, J.N. / Chung, Y.C. / Shim, H.K. / Lee, S.C. / Kwon, M.H. / Kim, Y.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Heavy and light chain variable single domains of an anti-DNA binding antibody hydrolyze both double- and single-stranded DNAs without sequence specificity. Authors: Kim, Y.R. / Kim, J.S. / Lee, S.H. / Lee, W.R. / Sohn, J.N. / Chung, Y.C. / Shim, H.K. / Lee, S.C. / Kwon, M.H. / Kim, Y.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gki.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gki.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/2gki ftp://data.pdbj.org/pub/pdb/validation_reports/gk/2gki | HTTPS FTP |
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-Related structure data
Related structure data | 1dzbS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Antibody | Mass: 31504.314 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pIg20 / Production host: Escherichia coli (E. coli) References: GenBank: 8777863, GenBank: 8777865, UniProt: A0N274*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.814426 Å3/Da / Density % sol: 81.950058 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2M Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→100 Å / Num. all: 40011 / Num. obs: 40011 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Rmerge(I) obs: 0.078 |
Reflection shell | Resolution: 2.88→2.98 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DZB Resolution: 2.88→49.58 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.88→49.58 Å
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