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Yorodumi- PDB-3bd4: Crystal structure of single domain VL of an anti-DNA binding anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bd4 | ||||||
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Title | Crystal structure of single domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals | ||||||
Components | catalytic antibody | ||||||
Keywords | IMMUNE SYSTEM / beta sandwich | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Park, S.K. / Kim, J.S. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals Authors: Park, S.Y. / Lee, W.R. / Lee, S.C. / Kwon, M.H. / Kim, Y.S. / Kim, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bd4.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bd4.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bd4_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 3bd4_full_validation.pdf.gz | 455.8 KB | Display | |
Data in XML | 3bd4_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 3bd4_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/3bd4 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/3bd4 | HTTPS FTP |
-Related structure data
Related structure data | 3bd3C 3bd5C 2gkiS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Antibody | Mass: 12460.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: 3d8 vl / Plasmid: pIg20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS #2: Chemical | #3: Chemical | ChemComp-BTB / | #4: 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: 2.04 Å3/Da / Density % sol: 39.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30 PEG 3350, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2006 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 8425 / Num. obs: 8273 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.062 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5 % / Rsym value: 0.553 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2GKI Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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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→2.45 Å
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