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Yorodumi- PDB-1dqd: CRYSTAL STRUCTURE OF FAB HGR-2 F6, A COMPETITIVE ANTAGONIST OF TH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dqd | ||||||
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Title | CRYSTAL STRUCTURE OF FAB HGR-2 F6, A COMPETITIVE ANTAGONIST OF THE GLUCAGON RECEPTOR | ||||||
Components | (FAB HGR-2 F6) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Glucagon receptor / monoclonal antibody / Fab / receptor antagonist / typical immunoglobulin fold / light chain / heavy chain / antigen binding site / complementarity-determining regions | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Wright, L.M. / Brzozowski, A.M. / Hubbard, R.E. / Pike, A.C.W. / Roberts, S.M. / Skovgaard, R.N. / Svendsen, I. / Vissing, H. / Bywater, R.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of Fab hGR-2 F6, a competitive antagonist of the glucagon receptor. Authors: Wright, L.M. / Brzozowski, A.M. / Hubbard, R.E. / Pike, A.C. / Roberts, S.M. / Skovgaard, R.N. / Svendsen, I. / Vissing, H. / Bywater, R.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dqd.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dqd.ent.gz | 81.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dqd_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 1dqd_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 1dqd_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 1dqd_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dqd ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dqd | 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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Unit cell |
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Details | The light chain and the heavy chain hydrogen bond together to form a single Fab monomer within the asymmetric unit. |
-Components
#1: Antibody | Mass: 23953.500 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN / Source method: isolated from a natural source Details: Using RBF mice, monoclonal antibodies were generated against the intact Human membrane-bound glucagon receptor. Fab fragments were produced from the intact IgG monoclonal antibody by papain ...Details: Using RBF mice, monoclonal antibodies were generated against the intact Human membrane-bound glucagon receptor. Fab fragments were produced from the intact IgG monoclonal antibody by papain digestion. Final purification of the Fab fragments was performed using both a MonoQ ion exchange column and subsequently a MonoS column. Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23892.545 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source Details: Using RBF mice, monoclonal antibodies were generated against the intact Human membrane-bound glucagon receptor. Fab fragments were produced from the intact IgG monoclonal antibody by papain ...Details: Using RBF mice, monoclonal antibodies were generated against the intact Human membrane-bound glucagon receptor. Fab fragments were produced from the intact IgG monoclonal antibody by papain digestion. Final purification of the Fab fragments was performed using both a MonoQ ion exchange column and subsequently a MonoS column. Source: (natural) Mus musculus (house mouse) |
#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: 1.99 Å3/Da / Density % sol: 38.25 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 24% (w/w) PEG 2KME, 100mM Tris HCl , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 173940 / Num. obs: 22946 / % possible obs: 98.1 % / Redundancy: 4 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.418 / Num. unique all: 1061 / % possible all: 95.4 |
Reflection | *PLUS Num. measured all: 173940 |
Reflection shell | *PLUS % possible obs: 95.4 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood method.
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.217 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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