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- PDB-6jwc: Mouse antibody 2B5 Fab in complex with PEG -

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Basic information

Entry
Database: PDB / ID: 6jwc
TitleMouse antibody 2B5 Fab in complex with PEG
Components(Immunoglobulin ...) x 2
KeywordsIMMUNE SYSTEM / antibody Fab / influenza hemagglutinin / complex structure / specific binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsLee, C.C. / Ko, T.P. / Su, Y.C. / Lin, L.L. / Roffler, S.R. / 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 19, 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
Revision 1.2Nov 20, 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
H: Immunoglobulin heavy chain Fab fragment
L: Immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,90414
Polymers47,4502
Non-polymers2,45512
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-86 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.895, 98.895, 96.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11H-777-

HOH

21H-796-

HOH

31L-560-

HOH

41L-565-

HOH

51L-575-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Immunoglobulin heavy chain Fab fragment


Mass: 23879.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Lentivirus
#2: Antibody Immunoglobulin light chain


Mass: 23570.080 Da / Num. of mol.: 1
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, 399 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H24O6
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.76 %

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 5, 2014
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 21952 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.954 / Rpim(I) all: 0.03 / Net I/σ(I): 25.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2123 / CC1/2: 0.808 / Rpim(I) all: 0.296 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JU0

6ju0


Resolution: 2.297→19.886 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 1100 5.03 %
Rwork0.187 --
obs0.1889 21890 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.297→19.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 154 387 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023495
X-RAY DIFFRACTIONf_angle_d0.6134717
X-RAY DIFFRACTIONf_dihedral_angle_d12.7382087
X-RAY DIFFRACTIONf_chiral_restr0.044506
X-RAY DIFFRACTIONf_plane_restr0.004575
LS refinement shellResolution: 2.3→2.4015 Å
RfactorNum. reflection% reflection
Rfree0.2743 136 -
Rwork0.2491 2499 -
obs--99 %

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