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- PDB-6h3h: Fab fragment of antibody against fullerene C60 -

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Basic information

Entry
Database: PDB / ID: 6h3h
TitleFab fragment of antibody against fullerene C60
Components
  • Anti-fullerene antibody Fab fragment Heavy chain
  • Anti-fullerene antibody Fab fragment Light chain
KeywordsIMMUNE SYSTEM / ANTIBODY FAB FULLERENE C60
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsOsipov, E.M. / Tikhonova, T.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-24-00172 Russian Federation
CitationJournal: Acta Naturae / Year: 2019
Title: Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding.
Authors: Osipov, E.M. / Hendrickson, O.D. / Tikhonova, T.V. / Zherdev, A.V. / Solopova, O.N. / Sveshnikov, P.G. / Dzantiev, B.B. / Popov, V.O.
History
DepositionJul 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-fullerene antibody Fab fragment Heavy chain
B: Anti-fullerene antibody Fab fragment Light chain
C: Anti-fullerene antibody Fab fragment Heavy chain
D: Anti-fullerene antibody Fab fragment Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,75514
Polymers93,8104
Non-polymers94510
Water8,215456
1
A: Anti-fullerene antibody Fab fragment Heavy chain
B: Anti-fullerene antibody Fab fragment Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2816
Polymers46,9052
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-44 kcal/mol
Surface area20080 Å2
MethodPISA
2
C: Anti-fullerene antibody Fab fragment Heavy chain
D: Anti-fullerene antibody Fab fragment Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4748
Polymers46,9052
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-71 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.330, 138.180, 83.530
Angle α, β, γ (deg.)90.00, 91.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Anti-fullerene antibody Fab fragment Heavy chain


Mass: 23775.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Spleen
#2: Antibody Anti-fullerene antibody Fab fragment Light chain


Mass: 23129.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: SPLEEN
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25 % w/v PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.98 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Feb 27, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.91→28.83 Å / Num. obs: 69665 / % possible obs: 99.5 % / Redundancy: 5 % / CC1/2: 0.999 / Rrim(I) all: 0.084 / Net I/σ(I): 17.5
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 4.8 % / Num. unique obs: 10963 / CC1/2: 0.83 / Rrim(I) all: 0.569 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSv2014data reduction
XSCALEv2014data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MFB

1mfb


Resolution: 1.92→28.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.271 / SU ML: 0.119 / SU R Cruickshank DPI: 0.16 / Cross valid method: FREE R-VALUE / ESU R: 0.158 / ESU R Free: 0.149 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.23354 3520 5.1 %RANDOM
Rwork0.18819 ---
obs0.19051 66144 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å2-0.23 Å2
2--0.4 Å20 Å2
3----1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.92→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6491 0 54 456 7001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026759
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.9459256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2375.011876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69124.174242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.547151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3921521
X-RAY DIFFRACTIONr_chiral_restr0.1320.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215013
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.7052.9073473
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7864.3344336
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.393.1083286
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.27139.59410059
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.915→1.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 254 -
Rwork0.277 4553 -
obs--94 %

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