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- PDB-8t7i: Structure of the S1CE variant of Fab F1 (FabS1CE-F1) -

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Entry
Database: PDB / ID: 8t7i
TitleStructure of the S1CE variant of Fab F1 (FabS1CE-F1)
Components(S1CE variant of Fab F1 ...) x 2
KeywordsIMMUNE SYSTEM / enhanced crystallization / EphA2 binding / expressed protein / Fab
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSinger, A.U. / Bruce, H.A. / Enderle, L. / Blazer, L. / Adams, J.J. / Sicheri, F. / Sidhu, S.S.
Funding support1items
OrganizationGrant numberCountry
Other private
Citation
Journal: Protein Sci. / Year: 2024
Title: Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes.
Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / ...Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / Atwell, S. / Kossiakoff, A.A. / Sidhu, S.S.
#1: Journal: J.Mol.Biol. / Year: 2018
Title: Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.
Authors: Bailey, L.J. / Sheehy, K.M. / Dominik, P.K. / Liang, W.G. / Rui, H. / Clark, M. / Jaskolowski, M. / Kim, Y. / Deneka, D. / Tang, W.J. / Kossiakoff, A.A.
#2: Journal: Plos One / Year: 2020
Title: Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing.
Authors: Lieu, R. / Antonysamy, S. / Druzina, Z. / Ho, C. / Kang, N.R. / Pustilnik, A. / Wang, J. / Atwell, S.
History
DepositionJun 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: S1CE variant of Fab F1 heavy chain
B: S1CE variant of Fab F1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,02714
Polymers48,6622
Non-polymers36512
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-122 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.000, 74.000, 219.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11B-304-

CL

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody S1CE variant of Fab F1 heavy chain


Mass: 25401.334 Da / Num. of mol.: 1 / Mutation: SSASTK replaced by FNQIK
Source method: isolated from a genetically manipulated source
Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody S1CE variant of Fab F1 light chain


Mass: 23260.754 Da / Num. of mol.: 1 / Mutation: spHAGLSSP replaced by QGTTS; Q165S, K167Y
Source method: isolated from a genetically manipulated source
Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 95 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% w/v PEG3350, 100 mM Bis-Tris propane, pH 6.5, 200 mM sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2022 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→74 Å / Num. obs: 20950 / % possible obs: 95 % / Redundancy: 6.4 % / Biso Wilson estimate: 42.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.074 / Rrim(I) all: 0.19 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.525 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2408 / CC1/2: 0.628 / Rpim(I) all: 0.635 / Rrim(I) all: 1.655 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DVN

3dvn


Resolution: 2.6→61.32 Å / SU ML: 0.2964 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2568 1467 7.92 %
Rwork0.2008 17058 -
obs0.2052 18525 94.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.35 Å2
Refinement stepCycle: LAST / Resolution: 2.6→61.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 15 83 3246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833231
X-RAY DIFFRACTIONf_angle_d1.08234411
X-RAY DIFFRACTIONf_chiral_restr0.0581498
X-RAY DIFFRACTIONf_plane_restr0.0071561
X-RAY DIFFRACTIONf_dihedral_angle_d16.84741091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.32071190.2741383X-RAY DIFFRACTION78.31
2.69-2.80.34221500.25351746X-RAY DIFFRACTION99.89
2.8-2.930.27581530.24171766X-RAY DIFFRACTION99.28
2.93-3.080.28271540.2291789X-RAY DIFFRACTION99.74
3.08-3.280.32391510.22211753X-RAY DIFFRACTION100
3.28-3.530.24181330.20541564X-RAY DIFFRACTION87.07
3.53-3.880.27671370.19741589X-RAY DIFFRACTION88.74
3.88-4.450.20131410.15691641X-RAY DIFFRACTION90.5
4.45-5.60.21081590.16671848X-RAY DIFFRACTION100
5.6-61.320.26241700.21181979X-RAY DIFFRACTION99.17
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)
11.79857458793-0.2143587621950.3745797713551.75457295919-1.132550191816.398006722690.08152707718140.904221366224-0.217547842786-1.222266820870.1760519845220.3201362929420.774892572004-0.116064808332-0.2173267662561.04924042188-0.122416452379-0.192951078130.63589009666-0.03577986198990.52426781993118.2587114734-7.7062317280419.7741206798
25.48586611482-0.523435713688-1.439633910140.554017398305-0.3452163109713.125883958370.0618740961133-0.1972370146510.1619884291390.1592474717470.02439899416890.220954584199-0.110632832258-0.00640887566799-0.0895569078090.299524770402-0.0243460637525-0.01916463536250.1664835765650.02850644932350.51011789970914.30888656132.9721123359952.969391371
34.3012536958-0.7481234447860.06360818408623.524174933441.519895290383.649922451720.05064741788520.7335939795930.635055969914-0.9417485904330.0998372682225-0.0752174495327-1.08362139757-0.290835441195-0.1110673412651.08257893923-0.0170015687138-0.1504090004630.7405584334960.185418039080.54205312198815.327159497713.304270022617.5433904468
41.668307947440.1558866972410.5906117995922.671613214321.410091023723.819050208790.02235983309510.1360129804760.225124618773-0.4750070321270.1517786489060.195949629012-0.3348292113150.106126147808-0.1841492776450.277764097169-0.0201813791065-0.01671189124010.1944715555740.03575276896330.47756195908523.490232990514.813464350248.2022728708
52.81915540151-0.8364891833491.529905577524.57403756804-0.1866707896734.70931427387-0.0597560597722-0.02084224527810.310939501778-0.0008428676644180.1456866295480.147110977284-0.341984740343-0.127861742692-0.07200655074150.205105392806-0.0113424058050.03948094634350.187941809651-0.002798451254920.3978554996624.590415451215.704321153653.2356944503
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 148 )AA1 - 1481 - 139
22chain 'A' and (resid 149 through 239 )AA149 - 239140 - 230
33chain 'B' and (resid 4 through 116 )BC4 - 1161 - 82
44chain 'B' and (resid 117 through 181 )BC117 - 18183 - 147
55chain 'B' and (resid 182 through 231 )BC182 - 231148 - 195

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