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- PDB-8dy3: Crystal Structure of spFv GLK2 HL -

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Basic information

Entry
Database: PDB / ID: 8dy3
TitleCrystal Structure of spFv GLK2 HL
ComponentsspFv GLK2 HL
KeywordsIMMUNE SYSTEM / scFv / stapled scFv / spFv / germline scFv / single chain Fv / scFv stabilizations / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.509 Å
Model detailsCrystal Structure of spFv GLK1 in LH configuration
AuthorsLuo, J. / Boucher, L.E.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Mabs / Year: 2023
Title: "Stapling" scFv for multispecific biotherapeutics of superior properties.
Authors: Boucher, L.E. / Prinslow, E.G. / Feldkamp, M. / Yi, F. / Nanjunda, R. / Wu, S.J. / Liu, T. / Lacy, E.R. / Jacobs, S. / Kozlyuk, N. / Del Rosario, B. / Wu, B. / Aquino, P. / Davidson, R.C. / ...Authors: Boucher, L.E. / Prinslow, E.G. / Feldkamp, M. / Yi, F. / Nanjunda, R. / Wu, S.J. / Liu, T. / Lacy, E.R. / Jacobs, S. / Kozlyuk, N. / Del Rosario, B. / Wu, B. / Aquino, P. / Davidson, R.C. / Heyne, S. / Mazzanti, N. / Testa, J. / Diem, M.D. / Gorre, E. / Mahan, A. / Nanda, H. / Gunawardena, H.P. / Gervais, A. / Armstrong, A.A. / Teplyakov, A. / Huang, C. / Zwolak, A. / Chowdhury, P. / Cheung, W.C. / Luo, J.
History
DepositionAug 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: spFv GLK2 HL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8403
Polymers26,6471
Non-polymers1922
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.030, 63.030, 124.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

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Components

#1: Antibody spFv GLK2 HL


Mass: 26647.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUNDER / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5 / Details: 100 mM Na Acetate, 750 mM (NH4)2 SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2018 / Details: mirrors
RadiationMonochromator: ACCEL SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.509→56.276 Å / Num. obs: 30532 / % possible obs: 94.2 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.027 / Rrim(I) all: 0.097 / Net I/σ(I): 17.3
Reflection shellResolution: 1.509→1.654 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.678 / Num. unique obs: 1527 / CC1/2: 0.513 / Rpim(I) all: 0.568 / Rrim(I) all: 1.777 / % possible all: 68.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3na9

3na9


Resolution: 1.509→56.276 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 1490 4.88 %
Rwork0.1831 29039 -
obs0.1844 30529 75.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.35 Å2 / Biso mean: 24.2488 Å2 / Biso min: 11.68 Å2
Refinement stepCycle: final / Resolution: 1.509→56.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 10 289 2089
Biso mean--48.34 33.83 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071851
X-RAY DIFFRACTIONf_angle_d0.9232518
X-RAY DIFFRACTIONf_chiral_restr0.061267
X-RAY DIFFRACTIONf_plane_restr0.005321
X-RAY DIFFRACTIONf_dihedral_angle_d12.1071089
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.509-1.55760.430790.27431665
1.5576-1.61330.2831270.293753015
1.6133-1.67790.2798640.2677130238
1.6779-1.75430.23211150.2448254173
1.7543-1.84680.28281720.2339339998
1.8468-1.96250.21871970.20313429100
1.9625-2.1140.21611850.18143475100
2.114-2.32680.19871600.1809335496
2.3268-2.66340.22561770.19243512100
2.6634-3.35560.2071800.18243580100
3.3556-56.2760.18782040.15933751100

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