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- PDB-4isv: Crystal structure of the Fab FRAGMENT OF 1C2, A MONOCLONAL ANTIBO... -

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Basic information

Entry
Database: PDB / ID: 4isv
TitleCrystal structure of the Fab FRAGMENT OF 1C2, A MONOCLONAL ANTIBODY SPECIFIC FOR POLY-GLUTAMINE
Components
  • 1C2 FAB HEAVY CHAIN
  • 1C2 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / 1C2 / Fab / Vlx / Neurodegeneration / Polyglutamine Disease / Amyloid Disease / Immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.497 Å
AuthorsKlein, F.A.C. / Zeder-Lutz, G. / Cousido-Siah, A. / Mitschler, A. / Katz, A. / Eberling, P. / Mandel, J.L. / Podjarny, A. / Trottier, Y.
CitationJournal: Hum.Mol.Genet. / Year: 2013
Title: Linear and extended: a common polyglutamine conformation recognized by the three antibodies MW1, 1C2 and 3B5H10.
Authors: Klein, F.A. / Zeder-Lutz, G. / Cousido-Siah, A. / Mitschler, A. / Katz, A. / Eberling, P. / Mandel, J.L. / Podjarny, A. / Trottier, Y.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Structure summary / Category: audit_author / software
Item: _audit_author.name / _software.classification ..._audit_author.name / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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

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Assembly

Deposited unit
A: 1C2 FAB LIGHT CHAIN
B: 1C2 FAB HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,4232
Polymers47,4232
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-23 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.785, 71.377, 90.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 1C2 FAB LIGHT CHAIN


Mass: 23479.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Cell (production host): MOUSE ASCITES FLUIDS FROM HYBRIDOMA CELLS
Production host: MUS MUSCULUS (house mouse)
#2: Antibody 1C2 FAB HEAVY CHAIN


Mass: 23943.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Cell (production host): MOUSE ASCITES FLUIDS FROM HYBRIDOMA CELLS
Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG3350, 100mM HEPES pH7.5; 1:1 volume with 1C2-Fab (10mg/ml) in 10mM TRIS, 10mM NaCl, pH7.3, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.90003 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90003 Å / Relative weight: 1
ReflectionResolution: 1.497→50 Å / Num. all: 64811 / Num. obs: 64811 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.048 / Χ2: 1.014 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.556.70.47163991.008198.4
1.55-1.626.80.34363771.01198.2
1.62-1.696.80.25364101.008198.7
1.69-1.786.80.16764251.041199
1.78-1.896.90.11164571.044198.9
1.89-2.046.90.07364830.976199
2.04-2.246.80.05765121.015199.5
2.24-2.566.80.05565801.012199.6
2.56-3.236.70.04166251199.7
3.23-506.30.02665431.023194.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1144refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.497→21.712 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8673 / SU ML: 0.13 / Cross valid method: R-free / σ(F): 0 / Phase error: 20.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 3283 5.07 %5% random
Rwork0.1981 ---
obs0.1991 64744 98.25 %-
all-64744 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.45 Å2 / Biso mean: 20.7696 Å2 / Biso min: 7.68 Å2
Refinement stepCycle: LAST / Resolution: 1.497→21.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 0 234 3514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073426
X-RAY DIFFRACTIONf_angle_d1.1664670
X-RAY DIFFRACTIONf_chiral_restr0.076529
X-RAY DIFFRACTIONf_plane_restr0.006592
X-RAY DIFFRACTIONf_dihedral_angle_d13.6841226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4973-1.51960.24111110.24562477258891
1.5196-1.54330.2931230.23052651277499
1.5433-1.56860.23241540.22332616277098
1.5686-1.59570.22561450.21232629277499
1.5957-1.62470.2221450.21052666281198
1.6247-1.65590.26261430.20762640278398
1.6559-1.68970.25321430.20762644278799
1.6897-1.72640.21821390.20172683282299
1.7264-1.76660.20971550.19782647280299
1.7666-1.81070.22991350.19742641277699
1.8107-1.85970.22951410.19552689283099
1.8597-1.91430.19891470.19492662280999
1.9143-1.97610.21831480.19042693284199
1.9761-2.04670.24151600.18932682284299
2.0467-2.12860.21491450.18612677282299
2.1286-2.22530.22671390.197727212860100
2.2253-2.34250.22471520.19782702285499
2.3425-2.48910.2311540.208626972851100
2.4891-2.6810.2621430.209227382881100
2.681-2.95020.2461330.201727582891100
2.9502-3.37570.18711490.189227532902100
3.3757-4.24780.18651460.1782757290398
4.2478-21.71420.20521330.20932638277190

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