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- PDB-8dy4: Crystal Structure of spFv CAT2200 HL -

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Basic information

Entry
Database: PDB / ID: 8dy4
TitleCrystal Structure of spFv CAT2200 HL
ComponentsspFv CAT2200 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: 2.4 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 20, 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: spFv CAT2200 HL


Theoretical massNumber of molelcules
Total (without water)26,6181
Polymers26,6181
Non-polymers00
Water00
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)63.340, 63.340, 104.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody spFv CAT2200 HL


Mass: 26618.316 Da / Num. of mol.: 1 / Fragment: spFv / Mutation: VL S43Q, VH T28G
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)
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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5 / Details: 100 mM Na Acetate, 1500 mM (NH4)2SO4

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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: 2.4→34.86 Å / Num. obs: 9924 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 64.432 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.081 / Χ2: 0.828 / Net I/σ(I): 15.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.461.2292.077170.9851.399.6
2.46-2.531.2592.337090.9831.32799.6
2.53-2.61.0942.566640.9741.15299.3
2.6-2.680.8143.126600.9910.85799.7
2.68-2.770.6283.986460.9880.66299.7
2.77-2.870.4275.16210.9940.4599.8
2.87-2.980.3116.266070.9970.32999.8
2.98-3.10.2377.815710.9980.25199.3
3.1-3.240.13311.185710.9990.141100
3.24-3.390.11713.455310.9990.12499.6
3.39-3.580.08318.995110.9990.088100
3.58-3.790.0819.934910.9990.085100
3.79-4.060.06526.274570.9990.069100
4.06-4.380.05231.024350.9990.056100
4.38-4.80.04239.13950.9990.045100
4.8-5.370.04141.523670.9990.043100
5.37-6.20.0442.2333010.043100
6.2-7.590.03544.722830.9990.037100
7.59-10.730.02848.832210.9990.03100
10.73-34.860.02647.9613710.02897.9

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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: 4QHU

4qhu


Resolution: 2.4→34.86 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 52.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3279 487 5.03 %
Rwork0.262 9195 -
obs0.265 9682 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.24 Å2 / Biso mean: 123.3044 Å2 / Biso min: 77.25 Å2
Refinement stepCycle: final / Resolution: 2.4→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 0 0 1739
Num. residues----234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.750.62271580.50682968312696
2.75-3.460.41331600.3412996315697
3.46-34.860.2741690.21143231340099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.37124.12780.7763.11851.1512.1570.08681.40870.22190.24140.78620.28540.70461.1336-1.04911.45710.3247-0.08321.4676-0.07061.046342.6735-18.0194-15.4614
26.47410.2297-1.13083.46921.7227.18710.16650.6541-0.67160.6860.7379-0.60520.79092.0787-0.52331.59970.6084-0.18211.2431-0.1470.9841.1434-17.2045-4.4167
34.1271-1.3538-0.66251.90383.1945.91560.1679-0.2636-0.14811.30810.669-0.55052.42041.8013-0.16771.68560.6118-0.23361.3801-0.13211.056441.3754-19.761-6.7985
47.99741.1341-1.77710.0941-0.8418.04290.3446-0.1036-1.8402-0.3470.24110.82333.3149-2.430610.61982.0172-0.006-0.09711.1479-0.07261.22423.3003-25.0639-5.5452
59.23450.42994.21742.01280.79369.44480.632-0.83481.21330.3143-0.56590.4470.467-1.17860.04321.38230.01310.16551.1398-0.15711.23621.7529-12.72740.2387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )A1 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 60 )A18 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 114 )A61 - 114
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 147 )A115 - 147
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 245 )A148 - 245

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