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Yorodumi- PDB-1dsf: THE CRYSTAL STRUCTURE OF THE DISULFIDE-STABILIZED FV FRAGMENT OF ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dsf | ||||||
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Title | THE CRYSTAL STRUCTURE OF THE DISULFIDE-STABILIZED FV FRAGMENT OF ANTICANCER ANTIBODY B1: CONFORMATIONAL INFLUENCE OF AN ENGINEERED DISULFIDE BOND | ||||||
Components | (ANTICANCER ANTIBODY B1) x 2 | ||||||
Keywords | IMMUNOGLOBULIN / MONOCLONAL ANTIBODY / ANTITUMOR | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Almog, O. / Gilliland, G.L. | ||||||
Citation | Journal: Proteins / Year: 1998 Title: Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: conformational influence of an engineered disulfide bond. Authors: Almog, O. / Benhar, I. / Vasmatzis, G. / Tordova, M. / Lee, B. / Pastan, I. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dsf.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dsf.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/1dsf ftp://data.pdbj.org/pub/pdb/validation_reports/ds/1dsf | HTTPS FTP |
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-Related structure data
Related structure data | 1iggS 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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Unit cell |
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-Components
#1: Antibody | Mass: 12223.854 Da / Num. of mol.: 1 / Fragment: FV / Mutation: CHAIN L, A100C, CHAIN H, R44C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: BL21 / Organ: SPLEEN / Plasmid: PB1VHR44C-STOP\ PB1VL A100C-STOP / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: PIR: B41940 |
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#2: Antibody | Mass: 13248.775 Da / Num. of mol.: 1 / Fragment: FV / Mutation: CHAIN L, A100C, CHAIN H, R44C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: BL21 / Organ: SPLEEN / Plasmid: PB1VHR44C-STOP\ PB1VL A100C-STOP / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) |
#3: 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: 2.6 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 1.6M HEPES PH-7.0 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→57.8 Å / Num. obs: 14289 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.108 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.12→2.2 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.2644 / % possible all: 58 |
Reflection | *PLUS Num. all: 15524 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.066 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IGG Resolution: 2→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Xplor file |
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