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- PDB-8iqs: Crystal structure of Anti-PEG antibody M11 Fv-clasp fragment with... -

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Basic information

Entry
Database: PDB / ID: 8iqs
TitleCrystal structure of Anti-PEG antibody M11 Fv-clasp fragment with PEG (co-crystallization with PEG3350)
Components
  • M11 VH-SARAH
  • M11 VL-SARAH
KeywordsIMMUNE SYSTEM
Function / homology3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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: To Be Published
Title: Comparation of structures and binding properties between two anti-polyethylene glycol antibodies induced via T cell-independent and T cell-dependent pathway
Authors: Liu, Y. / Mori, T. / Teramoto, T. / Kakuta, Y. / Mori, T.
History
DepositionMar 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: M11 VL-SARAH
H: M11 VH-SARAH
l: M11 VL-SARAH
h: M11 VH-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9808
Polymers84,0474
Non-polymers9334
Water1,54986
1
L: M11 VL-SARAH
H: M11 VH-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4904
Polymers42,0232
Non-polymers4662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-56 kcal/mol
Surface area16980 Å2
MethodPISA
2
l: M11 VL-SARAH
h: M11 VH-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4904
Polymers42,0232
Non-polymers4662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-51 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.330, 103.460, 174.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody M11 VL-SARAH


Mass: 20250.014 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)
#2: Antibody M11 VH-SARAH


Mass: 21773.465 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O9 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium sulfate, 20% (w/v) PEG 3350

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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: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→45.99 Å / Num. obs: 46727 / % possible obs: 100 % / Redundancy: 9.47 % / CC1/2: 0.999 / Rrim(I) all: 0.078 / Net I/σ(I): 18.55
Reflection shellResolution: 2.16→2.29 Å / Mean I/σ(I) obs: 0.91 / Num. unique obs: 7406 / CC1/2: 0.548 / Rrim(I) all: 2.293

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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: 2.16→44.84 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 1989 4.27 %
Rwork0.236 --
obs0.2374 46633 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5405 0 60 86 5551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.467
X-RAY DIFFRACTIONf_dihedral_angle_d19.2972099
X-RAY DIFFRACTIONf_chiral_restr0.039789
X-RAY DIFFRACTIONf_plane_restr0.003954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.42721400.41523123X-RAY DIFFRACTION99
2.21-2.270.48721490.44853153X-RAY DIFFRACTION99
2.27-2.340.44891410.36843146X-RAY DIFFRACTION100
2.34-2.420.33571280.34443161X-RAY DIFFRACTION100
2.42-2.50.33351570.3163135X-RAY DIFFRACTION100
2.5-2.60.36171320.29853181X-RAY DIFFRACTION100
2.6-2.720.31931410.29593167X-RAY DIFFRACTION100
2.72-2.860.32831420.30713162X-RAY DIFFRACTION100
2.86-3.040.34051440.29853205X-RAY DIFFRACTION100
3.04-3.280.33711400.26933164X-RAY DIFFRACTION100
3.28-3.610.27871450.25153206X-RAY DIFFRACTION100
3.61-4.130.30061430.21493230X-RAY DIFFRACTION100
4.13-5.20.18951400.17543238X-RAY DIFFRACTION100
5.21-44.840.19831470.18783373X-RAY DIFFRACTION100

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