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- PDB-1dqd: CRYSTAL STRUCTURE OF FAB HGR-2 F6, A COMPETITIVE ANTAGONIST OF TH... -

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Basic information

Entry
Database: PDB / ID: 1dqd
TitleCRYSTAL STRUCTURE OF FAB HGR-2 F6, A COMPETITIVE ANTAGONIST OF THE GLUCAGON RECEPTOR
Components(FAB HGR-2 F6) x 2
KeywordsIMMUNE SYSTEM / Glucagon receptor / monoclonal antibody / Fab / receptor antagonist / typical immunoglobulin fold / light chain / heavy chain / antigen binding site / complementarity-determining regions
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsWright, 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.
CitationJournal: 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
DepositionJan 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: FAB HGR-2 F6
H: FAB HGR-2 F6


Theoretical massNumber of molelcules
Total (without water)47,8462
Polymers47,8462
Non-polymers00
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-29 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.140, 133.740, 37.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe light chain and the heavy chain hydrogen bond together to form a single Fab monomer within the asymmetric unit.

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Components

#1: Antibody FAB HGR-2 F6


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)
#2: Antibody FAB HGR-2 F6


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 / water


Mass: 18.015 Da / Num. of mol.: 380 / Fragment: WATER / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris-HCl1drop
324 %(w/w)PEG MME20001reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood method.
RfactorNum. reflection% reflectionSelection details
Rfree0.315 1147 -RANDOM
Rwork0.217 ---
all-22946 --
obs-22425 98.1 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 0 380 3699
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.9

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