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- PDB-7x3n: Crystal structure of anti-mPEG h15-2b Fab -

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Basic information

Entry
Database: PDB / ID: 7x3n
TitleCrystal structure of anti-mPEG h15-2b Fab
Components
  • 15-2b-H
  • 15-2b-L
KeywordsIMMUNE SYSTEM / methoxy polyethylene glycol / mPEG / 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: 2.24 Å
AuthorsChang, C.Y. / Nguyen, T.M.T. / Toh, S.I. / Su, Y.C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)107-2113-M-009-021-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)109-2636-B-009-003 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.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
DepositionMar 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: 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 1.2Nov 13, 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-L
B: 15-2b-H
C: 15-2b-L
D: 15-2b-H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8686
Polymers96,2754
Non-polymers5932
Water6,233346
1
A: 15-2b-L
B: 15-2b-H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4343
Polymers48,1382
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-18 kcal/mol
Surface area19030 Å2
MethodPISA
2
C: 15-2b-L
D: 15-2b-H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4343
Polymers48,1382
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-20 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.930, 112.572, 158.821
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-L


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-H


Mass: 24598.355 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.: 346 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 18% (w/v) PEG 6000, 1% (w/v) PEG 2000 MME, 0.15 M lithium sulfate monohydrate, 0.1 M citric acid, pH 3.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. obs: 55882 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.926 / Net I/σ(I): 12.7
Reflection shellResolution: 2.24→2.34 Å / Num. unique obs: 6846 / CC1/2: 0.816 / % possible all: 99.6

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Processing

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

1l7i


Resolution: 2.24→27.61 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2693 --
Rwork0.2052 --
obs-52298 93.51 %
Displacement parametersBiso max: 88.75 Å2 / Biso mean: 25.7941 Å2 / Biso min: 4.11 Å2
Refinement stepCycle: LAST / Resolution: 2.24→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 40 346 6806
LS refinement shellResolution: 2.24→2.34 Å /
Num. reflection% reflection
obs6846 99.2 %

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