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- PDB-7y0g: Crystal structure of anti-mPEG h15-2b Fab -

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Basic information

Entry
Database: PDB / ID: 7y0g
TitleCrystal structure of anti-mPEG h15-2b Fab
Components
  • 15-2b 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: 2.08 Å
AuthorsChang, C.Y. / Nguyen, T.M.T. / Lin, E.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: Commun Chem / Year: 2022
Title: Structural determination of an antibody that specifically recognizes polyethylene glycol with a terminal methoxy group.
Authors: Nguyen, M.T. / Shih, Y.C. / Lin, M.H. / Roffler, S.R. / Hsiao, C.Y. / Cheng, T.L. / Lin, W.W. / Lin, E.C. / Jong, Y.J. / Chang, C.Y. / Su, Y.C.
History
DepositionJun 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 heavy chain
D: 15-2b light chain
E: 15-2b heavy chain
G: 15-2b light chain
H: 15-2b heavy chain
J: 15-2b light chain
K: 15-2b heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,73612
Polymers192,5508
Non-polymers1,1854
Water12,466692
1
A: 15-2b light chain
B: 15-2b heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4343
Polymers48,1382
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-19 kcal/mol
Surface area19260 Å2
MethodPISA
2
D: 15-2b light chain
E: 15-2b heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4343
Polymers48,1382
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-20 kcal/mol
Surface area19380 Å2
MethodPISA
3
G: 15-2b light chain
H: 15-2b heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4343
Polymers48,1382
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-19 kcal/mol
Surface area19300 Å2
MethodPISA
4
J: 15-2b light chain
K: 15-2b heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4343
Polymers48,1382
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-20 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.994, 112.285, 158.730
Angle α, β, γ (deg.)90.000, 90.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
15-2b light chain


Mass: 23539.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
15-2b heavy chain


Mass: 24598.355 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C13H28O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 3 Å3/Da / Density % sol: 58.98 %
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: BL13B1 / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 2.08→30 Å / Num. obs: 131932 / % possible obs: 98.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.77
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 12417 / CC1/2: 0.864 / CC star: 0.963 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L7I

1l7i


Resolution: 2.08→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.877 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 6507 5.1 %RANDOM
Rwork0.2109 ---
obs0.2126 121859 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.08 Å2 / Biso mean: 28.829 Å2 / Biso min: 12.06 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20.08 Å2
2---0.09 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 2.08→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12890 0 80 692 13662
Biso mean--38.45 31.1 -
Num. residues----1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01313286
X-RAY DIFFRACTIONr_bond_other_d0.0040.01812166
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.64918054
X-RAY DIFFRACTIONr_angle_other_deg1.3021.59228170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35751671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96623.404570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97152115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0711544
X-RAY DIFFRACTIONr_chiral_restr0.0480.21755
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022991
LS refinement shellResolution: 2.084→2.138 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 384 -
Rwork0.264 6844 -
all-7228 -
obs--73.75 %

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