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- PDB-4jj5: CRYSTAL STRUCTURE OF THE Fab FRAGMENT OF 1C2, A MONOCLONAL ANTIBO... -

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Basic information

Entry
Database: PDB / ID: 4jj5
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 / Vlx / Neurodegeneration / Polyglutamine Disease / Amyloid Disease / Immunoglobulin fold / Polyglutamine
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.445 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
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-26 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.464, 80.464, 180.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-335-

HOH

21B-348-

HOH

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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) / 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) / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.56 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7M MgSO4, 100mM MES 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

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2008
Details: 1.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION OF HARMONIC CONTAMINATION
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR UTILIZING A SI-111 AND SAGITAL HORIZONTAL FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.44→34.842 Å / Num. all: 25751 / Num. obs: 25751 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.5
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3.43 / Num. unique all: 2530 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ISV

4isv


Resolution: 2.445→34.842 Å / SU ML: 0.8 / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 1306 5.07 %random
Rwork0.2389 ---
all0.2411 25739 --
obs0.2411 25739 99.63 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.474 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5264 Å2-0 Å2-0 Å2
2--3.5264 Å2-0 Å2
3----7.0528 Å2
Refinement stepCycle: LAST / Resolution: 2.445→34.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 0 75 3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083083
X-RAY DIFFRACTIONf_angle_d1.1134188
X-RAY DIFFRACTIONf_dihedral_angle_d15.5591085
X-RAY DIFFRACTIONf_chiral_restr0.073480
X-RAY DIFFRACTIONf_plane_restr0.005524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4449-2.54280.35831370.2982652X-RAY DIFFRACTION100
2.5428-2.65850.32361520.27782671X-RAY DIFFRACTION100
2.6585-2.79860.39091500.28882668X-RAY DIFFRACTION100
2.7986-2.97380.39551420.29142711X-RAY DIFFRACTION100
2.9738-3.20330.28611640.26152662X-RAY DIFFRACTION100
3.2033-3.52540.2941270.25692712X-RAY DIFFRACTION100
3.5254-4.03480.27711380.222743X-RAY DIFFRACTION99
4.0348-5.0810.22691530.18892734X-RAY DIFFRACTION99
5.081-34.84550.25871430.23782880X-RAY DIFFRACTION99

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