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- PDB-6ju0: Mouse antibody 3.3 Fab in complex with PEG -

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Basic information

Entry
Database: PDB / ID: 6ju0
TitleMouse antibody 3.3 Fab in complex with PEG
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / antibody Fab / influenza hemagglutinin / complex structure / specific binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-PE3 / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsLee, C.C. / Ko, T.P. / Lin, L.L. / Wang, A.H.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: J.Biomed.Sci. / Year: 2020
Title: Structural basis of polyethylene glycol recognition by antibody.
Authors: Lee, C.C. / Su, Y.C. / Ko, T.P. / Lin, L.L. / Yang, C.Y. / Chang, S.S. / Roffler, S.R. / Wang, A.H.
History
DepositionApr 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
I: Fab heavy chain
M: Fab light chain
J: Fab heavy chain
N: Fab light chain
K: Fab heavy chain
O: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,31116
Polymers187,9538
Non-polymers2,3598
Water14,862825
1
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3914
Polymers46,9882
Non-polymers4022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-33 kcal/mol
Surface area19520 Å2
MethodPISA
2
I: Fab heavy chain
M: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7874
Polymers46,9882
Non-polymers7992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-27 kcal/mol
Surface area19370 Å2
MethodPISA
3
J: Fab heavy chain
N: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1523
Polymers46,9882
Non-polymers1641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-35 kcal/mol
Surface area19480 Å2
MethodPISA
4
K: Fab heavy chain
O: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9815
Polymers46,9882
Non-polymers9933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-25 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.299, 177.347, 89.019
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 8 molecules HIJKLMNO

#1: Antibody
Fab heavy chain / Fragment antigen-binding


Mass: 23691.459 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Lentivirus
#2: Antibody
Fab light chain / Fragment antigen-binding


Mass: 23296.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Lentivirus

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Non-polymers , 5 types, 833 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H16O4
#5: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol


Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O15
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 825 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, 2-propanol, PEG 2000 MME, Ni-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 64434 / % possible obs: 98.6 % / Redundancy: 3.1 % / CC1/2: 0.928 / Rpim(I) all: 0.052 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6420 / CC1/2: 0.699 / Rpim(I) all: 0.361 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W9D

3w9d


Resolution: 2.601→24.503 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 1975 3.1 %
Rwork0.2108 --
obs0.2117 63647 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→24.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13044 0 141 826 14011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213548
X-RAY DIFFRACTIONf_angle_d0.68618401
X-RAY DIFFRACTIONf_dihedral_angle_d13.138094
X-RAY DIFFRACTIONf_chiral_restr0.0462026
X-RAY DIFFRACTIONf_plane_restr0.0052308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6006-2.66550.34991070.29953616X-RAY DIFFRACTION79
2.6655-2.73750.33471480.29264289X-RAY DIFFRACTION95
2.7375-2.8180.34311400.28674438X-RAY DIFFRACTION98
2.818-2.90880.28621450.27224503X-RAY DIFFRACTION99
2.9088-3.01260.29411480.2714504X-RAY DIFFRACTION99
3.0126-3.1330.31651370.26324497X-RAY DIFFRACTION99
3.133-3.27520.25981490.24224511X-RAY DIFFRACTION99
3.2752-3.44750.25621370.22794521X-RAY DIFFRACTION99
3.4475-3.66280.23591450.20974491X-RAY DIFFRACTION99
3.6628-3.94450.23431490.20014496X-RAY DIFFRACTION99
3.9445-4.33950.21681460.17454488X-RAY DIFFRACTION99
4.3395-4.96290.17951440.15654472X-RAY DIFFRACTION98
4.9629-6.23560.19591330.17464452X-RAY DIFFRACTION98
6.2356-24.50370.21651470.19144394X-RAY DIFFRACTION95

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