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- PDB-6qkd: CRYSTAL STRUCTURE OF vhh-based FAB-fragment of antibody BCD-085 -

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Basic information

Entry
Database: PDB / ID: 6qkd
TitleCRYSTAL STRUCTURE OF vhh-based FAB-fragment of antibody BCD-085
Components
  • FAB HEAVY CHAINFragment antigen-binding
  • FAB LIGHT CHAINFragment antigen-binding
KeywordsIMMUNE SYSTEM / VHH / Fab fragment / BCD-085 antibody / complementarity determining regions / IL-17A / psoriasis
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKostareva, O.S. / Kolyadenko, I.A. / Ulitin, A.B. / Ekimova, V.M. / Evdokimov, S.R. / Garber, M.B. / Tishchenko, T.V. / Gabdulkhakov, A.G.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation17-74-10156 Russian Federation
CitationJournal: Crystals / Year: 2019
Title: Fab Fragment of VHH-Based Antibody Netakimab: Crystal Structure and Modeling Interaction with Cytokine IL-17A
Authors: Kostareva, O.S. / Kolyadenko, I.A. / Ulitin, A.B. / Ekimova, V.M. / Evdokimov, S.R. / Garber, M.B. / Tishchenko, T.V. / Gabdulkhakov, A.G.
History
DepositionJan 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: FAB HEAVY CHAIN
I: FAB HEAVY CHAIN
J: FAB HEAVY CHAIN
K: FAB HEAVY CHAIN
L: FAB LIGHT CHAIN
M: FAB LIGHT CHAIN
O: FAB LIGHT CHAIN
T: FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,79021
Polymers189,7238
Non-polymers1,06713
Water5,693316
1
H: FAB HEAVY CHAIN
L: FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7195
Polymers47,4312
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-46 kcal/mol
Surface area20630 Å2
MethodPISA
2
I: FAB HEAVY CHAIN
T: FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6946
Polymers47,4312
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-48 kcal/mol
Surface area20910 Å2
MethodPISA
3
J: FAB HEAVY CHAIN
M: FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6234
Polymers47,4312
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-34 kcal/mol
Surface area21130 Å2
MethodPISA
4
K: FAB HEAVY CHAIN
O: FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7546
Polymers47,4312
Non-polymers3244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-51 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.560, 111.920, 165.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody
FAB HEAVY CHAIN / Fragment antigen-binding


Mass: 23906.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
FAB LIGHT CHAIN / Fragment antigen-binding


Mass: 23524.033 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM Na-Ac pH 5.5, 150 mM NaCl with 1.5 M (NH4)2SO4, 150 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 132510 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.2
Reflection shellResolution: 1.9→1.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I1K, 5FGB

5i1k

5fgb


Resolution: 1.9→47.6 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / SU B: 11.821 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22802 6624 5 %RANDOM
Rwork0.16872 ---
obs0.17173 125855 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.813 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å2-0 Å2
2---0.65 Å2-0 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.9→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13122 0 53 316 13491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213560
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212395
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.95718442
X-RAY DIFFRACTIONr_angle_other_deg1.186328659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41851746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04223.642530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.823152105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3091574
X-RAY DIFFRACTIONr_chiral_restr0.070.22067
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115404
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023070
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_it6.4284.7656999
X-RAY DIFFRACTIONr_mcbond_other6.4264.7646998
X-RAY DIFFRACTIONr_mcangle_it7.7877.1418740
X-RAY DIFFRACTIONr_mcangle_other7.7877.1418741
X-RAY DIFFRACTIONr_scbond_it6.7945.0526561
X-RAY DIFFRACTIONr_scbond_other6.6075.0296522
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0557.3999643
X-RAY DIFFRACTIONr_long_range_B_refined9.19838.23414352
X-RAY DIFFRACTIONr_long_range_B_other9.16938.214295
X-RAY DIFFRACTIONr_rigid_bond_restr6.738325955
X-RAY DIFFRACTIONr_sphericity_free32.7815113
X-RAY DIFFRACTIONr_sphericity_bonded21.487525851
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 471 -
Rwork0.318 8961 -
obs--97.37 %

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