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- PDB-8z95: Humanized anti-PEG h6.3 Fab in complex with PEG -

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Basic information

Entry
Database: PDB / ID: 8z95
TitleHumanized anti-PEG h6.3 Fab in complex with PEG
Components
  • Heavy chain of Anti-PEG antibody h6-3 Fab fragment
  • Light chain of Anti-PEG antibody h6-3 Fab fragment
KeywordsIMMUNE SYSTEM / Anti-PEG / Fab
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsLin, Y.C. / Chang, C.Y. / Su, Y.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Acs Nano / Year: 2025
Title: pH-Responsive Polyethylene Glycol Engagers for Enhanced Brain Delivery of PEGylated Nanomedicine to Treat Glioblastoma.
Authors: Meng, J.L. / Dong, Z.X. / Chen, Y.R. / Lin, M.H. / Liu, Y.C. / Roffler, S.R. / Lin, W.W. / Chang, C.Y. / Tzou, S.C. / Cheng, T.L. / Huang, H.C. / Li, Z.Q. / Lin, Y.C. / Su, Y.C.
History
DepositionApr 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heavy chain of Anti-PEG antibody h6-3 Fab fragment
B: Light chain of Anti-PEG antibody h6-3 Fab fragment
H: Heavy chain of Anti-PEG antibody h6-3 Fab fragment
L: Light chain of Anti-PEG antibody h6-3 Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3766
Polymers95,0944
Non-polymers1,2822
Water3,243180
1
A: Heavy chain of Anti-PEG antibody h6-3 Fab fragment
B: Light chain of Anti-PEG antibody h6-3 Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8294
Polymers47,5472
Non-polymers1,2822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-21 kcal/mol
Surface area19730 Å2
MethodPISA
2
H: Heavy chain of Anti-PEG antibody h6-3 Fab fragment
L: Light chain of Anti-PEG antibody h6-3 Fab fragment


Theoretical massNumber of molelcules
Total (without water)47,5472
Polymers47,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-33 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)245.365, 43.574, 110.148
Angle α, β, γ (deg.)90.00, 111.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Heavy chain of Anti-PEG antibody h6-3 Fab fragment


Mass: 23447.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Heavy chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Light chain of Anti-PEG antibody h6-3 Fab fragment


Mass: 24099.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: light chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C55H112O28 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% (w/v) PEG-6000, 1% (w/v) PEG-2000-methyl ether, 0.15 M lithium sulfate monohydrate, and 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→30 Å / Num. obs: 50690 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rrim(I) all: 0.053 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.27-2.353.70.33349890.90.9730.2020.3910.84899.2
2.35-2.453.70.27350780.9290.9810.1640.3190.86799.7
2.45-2.563.80.20150740.9580.9890.1210.2350.87799.9
2.56-2.693.70.14550360.9770.9940.0870.1690.89999.8
2.69-2.863.70.10250210.9870.9970.0610.1190.9499.7
2.86-3.083.70.06950750.9930.9980.0420.0810.97699.3
3.08-3.393.60.04450680.9960.9990.0270.0521.02598.9
3.39-3.883.50.02850640.99810.0180.0330.94998.9
3.88-4.883.50.0250760.99910.0130.0240.88298.2
4.88-303.30.01852090.99910.0120.0220.73297.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
SCALAdata scaling
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VL9

6vl9


Resolution: 2.26→29.81 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.606 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26148 2611 5.2 %RANDOM
Rwork0.20944 ---
obs0.21214 48044 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0.1 Å2
2---0.09 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.26→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 74 180 6790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126776
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166224
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6529206
X-RAY DIFFRACTIONr_angle_other_deg0.5321.59114422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0695848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.565520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.166101065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021506
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1723.8163410
X-RAY DIFFRACTIONr_mcbond_other3.1723.8163410
X-RAY DIFFRACTIONr_mcangle_it4.7616.844252
X-RAY DIFFRACTIONr_mcangle_other4.7616.844253
X-RAY DIFFRACTIONr_scbond_it3.4264.0033366
X-RAY DIFFRACTIONr_scbond_other3.4264.0053367
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3087.2334955
X-RAY DIFFRACTIONr_long_range_B_refined7.1635.887070
X-RAY DIFFRACTIONr_long_range_B_other7.15835.827055
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.265→2.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 176 -
Rwork0.257 3387 -
obs--96.45 %

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