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- PDB-7yiz: Crystal structure of anti-mPEG h15-2b Fab W104Y mutant -

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Basic information

Entry
Database: PDB / ID: 7yiz
TitleCrystal structure of anti-mPEG h15-2b Fab W104Y mutant
Components
  • 15-2b W104Y heavy chain
  • 15-2b light chain
KeywordsIMMUNE SYSTEM / methoxy polyethylene glycol / anti-mPEG antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsChang, C.Y. / Nguyen, T.M.T. / Li, Y.C. / Su, Y.C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST109-2636-B-009-003 Taiwan
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-A49-026-MY3 Taiwan
CitationJournal: Bioconjug.Chem. / Year: 2022
Title: Engineering a High-Affinity Anti-Methoxy Poly(ethylene glycol) (mPEG) Antibody for Sensitive Immunosensing of mPEGylated Therapeutics and mPEG Molecules
Authors: Hsiao, C.Y. / Meng, J.L. / Hong, J.Z. / Ly, X.H. / Lin, M.H. / Chang, C.Y. / Nguyen, M.T.T. / Cheng, T.L. / Lin, W.W. / Burnouf, P.A. / Al-Qaisi, T.S. / Liu, E.S. / Su, Y.C.
History
DepositionJul 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 15-2b light chain
B: 15-2b W104Y heavy chain
C: 15-2b light chain
D: 15-2b W104Y heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8226
Polymers96,2294
Non-polymers5932
Water1,856103
1
A: 15-2b light chain
B: 15-2b W104Y heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4113
Polymers48,1142
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-16 kcal/mol
Surface area19410 Å2
MethodPISA
2
C: 15-2b light chain
D: 15-2b W104Y heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4113
Polymers48,1142
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-20 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.335, 112.056, 157.792
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 15-2b light chain


Mass: 23539.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 15-2b W104Y heavy chain


Mass: 24575.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H28O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% (w/v) PEG-6000, 1% (w/v) PEG-2000-MME, 0.15 M lithium sulfate monohydrate, and 0.1 M citric acid

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→30 Å / Num. obs: 42950 / % possible obs: 98.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.135
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3809 / % possible all: 89.5

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y0G

7y0g


Resolution: 2.42→29.81 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.562 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 1986 4.9 %RANDOM
Rwork0.2156 ---
obs0.2183 38141 91.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.52 Å2 / Biso mean: 37.099 Å2 / Biso min: 14.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å20 Å2
2---0.3 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 2.42→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 40 103 6608
Biso mean--50.96 29.26 -
Num. residues----845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136660
X-RAY DIFFRACTIONr_bond_other_d0.0040.0186101
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.659046
X-RAY DIFFRACTIONr_angle_other_deg1.2941.59314129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7915839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80323.404285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1031522
X-RAY DIFFRACTIONr_chiral_restr0.0550.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021496
LS refinement shellResolution: 2.42→2.48 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.348 105 -
Rwork0.263 1861 -
obs--62.1 %

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