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- PDB-2gsg: Crystal structure of the Fv fragment of a monoclonal antibody spe... -

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Basic information

Entry
Database: PDB / ID: 2gsg
TitleCrystal structure of the Fv fragment of a monoclonal antibody specific for poly-glutamine
Components
  • monoclonal antibody heavy chain
  • monoclonal antibody light chain
KeywordsIMMUNE SYSTEM / Fv / monoclonal antibody / poly-glutamine
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, P. / Huey-Tubman, K.E. / West Jr., A.P. / Bennett, M.J. / Bjorkman, P.J.
CitationJournal: 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
DepositionApr 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: monoclonal antibody light chain
B: monoclonal antibody heavy chain
C: monoclonal antibody light chain
D: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9507
Polymers51,6624
Non-polymers2883
Water5,386299
1
A: monoclonal antibody light chain
B: monoclonal antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1195
Polymers25,8312
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-42 kcal/mol
Surface area11170 Å2
MethodPISA
2
C: monoclonal antibody light chain
D: monoclonal antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)25,8312
Polymers25,8312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-12 kcal/mol
Surface area11180 Å2
MethodPISA
3
A: monoclonal antibody light chain
B: monoclonal antibody heavy chain
hetero molecules

C: monoclonal antibody light chain
D: monoclonal antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)51,9507
Polymers51,6624
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+1/2,y-1/2,-z1
Buried area5640 Å2
ΔGint-71 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.876, 78.096, 50.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody monoclonal antibody light chain


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 monoclonal antibody heavy chain


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 ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
MOLREPphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.253 3517 Random
Rwork0.229 --
all0.229 38667 -
obs0.229 35517 -
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 15 299 3926

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