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Yorodumi- PDB-2gsg: Crystal structure of the Fv fragment of a monoclonal antibody spe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gsg | ||||||
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Title | Crystal structure of the Fv fragment of a monoclonal antibody specific for poly-glutamine | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fv / monoclonal antibody / poly-glutamine | ||||||
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: 2.1 Å | ||||||
Authors | Li, P. / Huey-Tubman, K.E. / West Jr., A.P. / Bennett, M.J. / Bjorkman, P.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: The structure of a polyQ-anti-polyQ complex reveals binding according to a linear lattice model. Authors: Li, P. / Huey-Tubman, K.E. / Gao, T. / Li, X. / West Jr., A.P. / Bennett, M.J. / Bjorkman, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gsg.cif.gz | 103.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gsg.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 2gsg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gsg_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 2gsg_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 2gsg_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 2gsg_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/2gsg ftp://data.pdbj.org/pub/pdb/validation_reports/gs/2gsg | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 12499.897 Da / Num. of mol.: 2 / Fragment: variable domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Antibody | Mass: 13330.936 Da / Num. of mol.: 2 / Fragment: variable domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #3: Chemical | #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: 3.12 Å3/Da / Density % sol: 60.57 % |
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Crystal grow | Temperature: 290 K / Method: evaporation / pH: 6.5 Details: 0.1M sodium cacodylate, pH 6.5, 20% PEG 8000, 0.2M (NH4)2SO4, EVAPORATION, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2004 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 38667 / Num. obs: 37635 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.068 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3303 / Rsym value: 0.444 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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