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- PDB-8dy0: Crystal Structure of spFv GLK1 HL -

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Basic information

Entry
Database: PDB / ID: 8dy0
TitleCrystal Structure of spFv GLK1 HL
ComponentsspFv GLK1 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: 2.1 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: spFv GLK1 HL
B: spFv GLK1 HL


Theoretical massNumber of molelcules
Total (without water)53,1232
Polymers53,1232
Non-polymers00
Water3,243180
1
A: spFv GLK1 HL


Theoretical massNumber of molelcules
Total (without water)26,5611
Polymers26,5611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: spFv GLK1 HL


Theoretical massNumber of molelcules
Total (without water)26,5611
Polymers26,5611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.940, 50.740, 63.200
Angle α, β, γ (deg.)76.350, 89.200, 69.160
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 61 or (resid 62...
21(chain B and (resid 1 through 61 or (resid 62...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALA(chain A and (resid 1 through 61 or (resid 62...AA1 - 611 - 61
12ASPASPASPASP(chain A and (resid 1 through 61 or (resid 62...AA6262
13GLUGLULYSLYS(chain A and (resid 1 through 61 or (resid 62...AA1 - 2441 - 244
14GLUGLULYSLYS(chain A and (resid 1 through 61 or (resid 62...AA1 - 2441 - 244
15GLUGLULYSLYS(chain A and (resid 1 through 61 or (resid 62...AA1 - 2441 - 244
16GLUGLULYSLYS(chain A and (resid 1 through 61 or (resid 62...AA1 - 2441 - 244
17GLUGLULYSLYS(chain A and (resid 1 through 61 or (resid 62...AA1 - 2441 - 244
18GLUGLULYSLYS(chain A and (resid 1 through 61 or (resid 62...AA1 - 2441 - 244
21GLUGLUALAALA(chain B and (resid 1 through 61 or (resid 62...BB1 - 611 - 61
22ASPASPASPASP(chain B and (resid 1 through 61 or (resid 62...BB6262
23GLUGLULYSLYS(chain B and (resid 1 through 61 or (resid 62...BB1 - 2441 - 244
24GLUGLULYSLYS(chain B and (resid 1 through 61 or (resid 62...BB1 - 2441 - 244
25GLUGLULYSLYS(chain B and (resid 1 through 61 or (resid 62...BB1 - 2441 - 244
26GLUGLULYSLYS(chain B and (resid 1 through 61 or (resid 62...BB1 - 2441 - 244
27GLUGLULYSLYS(chain B and (resid 1 through 61 or (resid 62...BB1 - 2441 - 244
28GLUGLULYSLYS(chain B and (resid 1 through 61 or (resid 62...BB1 - 2441 - 244

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Components

#1: Antibody spFv GLK1 HL


Mass: 26561.365 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5 / Details: 100 mM MES, 750 mM (NH4)2SO4, 5% PEG 400

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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: 2.1→35.35 Å / Num. obs: 24805 / % possible obs: 99.5 % / Redundancy: 5.36 % / Biso Wilson estimate: 36.761 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.167 / Χ2: 0.961 / Net I/σ(I): 7.38 / Num. measured all: 132954 / Scaling rejects: 180
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.153.3860.6072.3318400.8280.72199.2
2.15-2.213.310.5452.4817650.8270.64998.2
2.21-2.283.2930.4592.817120.8850.54899.1
2.28-2.354.9120.5423.3416880.8740.60799.1
2.35-2.426.0640.5313.8616460.9150.58199.6
2.42-2.515.9790.4344.5415880.9470.47699.7
2.51-2.66.1570.385.1215060.9530.41699.7
2.6-2.716.0150.3155.815140.9640.34599.3
2.71-2.836.140.2716.8314050.9770.296100
2.83-2.975.9690.2167.7713430.9830.237100
2.97-3.136.1030.1828.9912950.980.299.7
3.13-3.325.9730.15210.6312060.9870.16799.9
3.32-3.555.9510.12712.0511340.9870.13999.3
3.55-3.835.9560.11813.1710710.990.12999.9
3.83-4.25.9060.10914.019870.990.11999.8
4.2-4.75.7760.115.098820.9880.1199.2
4.7-5.425.8010.09515.127730.9880.104100
5.42-6.646.1690.10215.36630.9930.111100
6.64-9.395.9550.09115.645080.9940.09999.6
9.39-35.356.0820.116.892790.990.10999.6

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3na9

3na9


Resolution: 2.1→35.35 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 1238 4.99 %
Rwork0.182 23551 -
obs0.1842 24789 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.53 Å2 / Biso mean: 34.7036 Å2 / Biso min: 17.03 Å2
Refinement stepCycle: final / Resolution: 2.1→35.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 0 180 3744
Biso mean---37.08 -
Num. residues----487
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2077X-RAY DIFFRACTION8.581TORSIONAL
12B2077X-RAY DIFFRACTION8.581TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.180.32751370.2572592272999
2.18-2.280.30511360.24252598273499
2.28-2.40.30411380.22782618275699
2.4-2.550.29031380.211926282766100
2.55-2.750.23991380.213926142752100
2.75-3.030.24441370.201826112748100
3.03-3.470.24131390.176226432782100
3.47-4.370.16451370.149326172754100
4.37-35.350.17241380.148126302768100

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