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- PDB-8iqp: Crystal structure of Anti-PEG antibody M9 Fv-clasp fragment with ... -

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Basic information

Entry
Database: PDB / ID: 8iqp
TitleCrystal structure of Anti-PEG antibody M9 Fv-clasp fragment with PEG (co-crystallization with PEG3350)
Components
  • M9 VH-SARAH
  • M9 VL-SARAH
KeywordsIMMUNE SYSTEM
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsMori, T. / Teramoto, T. / Liu, Y. / Mori, T. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J Control Release / Year: 2025
Title: The strategy used by naive anti-PEG antibodies to capture flexible and featureless PEG chains.
Authors: Liu, Y. / Mori, T. / Ito, Y. / Kuroki, K. / Hayashi, S. / Kohda, D. / Shimizu, T. / Ishida, T. / Roffler, S.R. / Kaneko, M.K. / Kato, Y. / Arimori, T. / Teramoto, T. / Takemura, K. / ...Authors: Liu, Y. / Mori, T. / Ito, Y. / Kuroki, K. / Hayashi, S. / Kohda, D. / Shimizu, T. / Ishida, T. / Roffler, S.R. / Kaneko, M.K. / Kato, Y. / Arimori, T. / Teramoto, T. / Takemura, K. / Ishibashi, K. / Katayama, Y. / Maenaka, K. / Kakuta, Y. / Kitao, A. / Mori, T.
History
DepositionMar 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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
Revision 1.3Mar 26, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: M9 VL-SARAH
H: M9 VH-SARAH
l: M9 VL-SARAH
h: M9 VH-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4946
Polymers82,4014
Non-polymers1,0932
Water8,017445
1
L: M9 VL-SARAH
H: M9 VH-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7473
Polymers41,2012
Non-polymers5471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-45 kcal/mol
Surface area16670 Å2
MethodPISA
2
l: M9 VL-SARAH
h: M9 VH-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7473
Polymers41,2012
Non-polymers5471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-42 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.230, 68.340, 94.790
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody M9 VL-SARAH


Mass: 20273.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MSKIKGHHHHHHGG is derived from plasmid. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody M9 VH-SARAH


Mass: 20927.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MSKIKGHHHHHHGG is derived from expression plasmid. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium acetate and 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→45.95 Å / Num. obs: 71343 / % possible obs: 99.6 % / Redundancy: 3.22 % / CC1/2: 0.995 / Rrim(I) all: 0.105 / Net I/σ(I): 5.54
Reflection shellResolution: 1.76→1.86 Å / Mean I/σ(I) obs: 0.55 / Num. unique obs: 11764 / CC1/2: 0.602 / Rrim(I) all: 1.415

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→45.95 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1984 2.79 %
Rwork0.2054 --
obs0.2065 70984 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5320 0 71 445 5836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.896
X-RAY DIFFRACTIONf_dihedral_angle_d8.254788
X-RAY DIFFRACTIONf_chiral_restr0.053786
X-RAY DIFFRACTIONf_plane_restr0.007939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.44941400.454676X-RAY DIFFRACTION96
1.8-1.850.40421350.39754922X-RAY DIFFRACTION99
1.85-1.910.37841360.35174899X-RAY DIFFRACTION99
1.91-1.970.36821430.32874909X-RAY DIFFRACTION100
1.97-2.040.33561410.28714928X-RAY DIFFRACTION99
2.04-2.120.30581440.2574916X-RAY DIFFRACTION99
2.12-2.220.28521350.23224953X-RAY DIFFRACTION99
2.22-2.330.2911510.21834927X-RAY DIFFRACTION100
2.33-2.480.26481450.21734907X-RAY DIFFRACTION99
2.48-2.670.28031370.22334958X-RAY DIFFRACTION100
2.67-2.940.24221440.21674957X-RAY DIFFRACTION100
2.94-3.370.24171440.20344977X-RAY DIFFRACTION99
3.37-4.240.23431420.1634988X-RAY DIFFRACTION100
4.24-45.950.16811470.15675083X-RAY DIFFRACTION100

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