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- PDB-8vua: Structure of FabS1CE1-EPR-1, an elbow-locked high affinity antibo... -

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Basic information

Entry
Database: PDB / ID: 8vua
TitleStructure of FabS1CE1-EPR-1, an elbow-locked high affinity antibody for the erythropoeitin receptor
Components
  • S1CE1 VARIANT OF FAB-EPR-1 heavy chain
  • S1CE1 VARIANT OF FAB-EPR-1 light chain
KeywordsIMMUNE SYSTEM / proliferation / engineered antibody / high-affinity binding / enhanced crystallization
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsSinger, A.U. / Bruce, H.A. / Pavlenco, A. / Ploder, L. / Luu, G. / Blazer, L. / Adams, J.J. / Sidhu, S.S.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159640 Canada
Other private
CitationJournal: Protein Sci. / Year: 2024
Title: Antigen-binding fragments with improved crystal lattice packing and enhanced conformational flexibility at the elbow region as crystallization chaperones.
Authors: Bruce, H.A. / Singer, A.U. / Blazer, L.L. / Luu, K. / Ploder, L. / Pavlenco, A. / Kurinov, I. / Adams, J.J. / Sidhu, S.S.
History
DepositionJan 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: S1CE1 VARIANT OF FAB-EPR-1 light chain
A: S1CE1 VARIANT OF FAB-EPR-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0732
Polymers47,0732
Non-polymers00
Water00
1
G: S1CE1 VARIANT OF FAB-EPR-1 light chain
A: S1CE1 VARIANT OF FAB-EPR-1 heavy chain

G: S1CE1 VARIANT OF FAB-EPR-1 light chain
A: S1CE1 VARIANT OF FAB-EPR-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)94,1474
Polymers94,1474
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area7590 Å2
ΔGint-54 kcal/mol
Surface area36420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.933, 72.933, 153.366
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Antibody S1CE1 VARIANT OF FAB-EPR-1 light chain


Mass: 23049.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND COMPND 7 SELECTED BY PHAGE DISPLAY. FABS UTILIZE IMGT (LECLERC ET AL., DEV COMPND 8 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 S1CE1 VARIANT OF FAB-EPR-1 heavy chain


Mass: 24023.959 Da / Num. of mol.: 1 / Mutation: E162G
Source method: isolated from a genetically manipulated source
Details: FAB PRODUCED BY RANDOMIZATION OF CDR REGIONS AND COMPND 7 SELECTED BY PHAGE DISPLAY. FABS UTILIZE IMGT (LECLERC ET AL., DEV COMPND 8 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES 7.0, 30% Jeffamine ED-2003 / Temp details: room temperature

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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 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.13→153.37 Å / Num. obs: 8839 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 139.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.025 / Rrim(I) all: 0.078 / Net I/σ(I): 19.5
Reflection shellResolution: 3.13→3.35 Å / Redundancy: 10.5 % / Rmerge(I) obs: 2.017 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1569 / CC1/2: 0.505 / Rpim(I) all: 0.651 / Rrim(I) all: 2.121 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.27→58.4 Å / SU ML: 0.4966 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2823 403 5.21 %
Rwork0.2454 7338 -
obs0.2472 7741 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 143.82 Å2
Refinement stepCycle: LAST / Resolution: 3.27→58.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 0 0 3137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323210
X-RAY DIFFRACTIONf_angle_d0.60944392
X-RAY DIFFRACTIONf_chiral_restr0.0432508
X-RAY DIFFRACTIONf_plane_restr0.0125565
X-RAY DIFFRACTIONf_dihedral_angle_d5.0143462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.27-3.740.3571330.38292381X-RAY DIFFRACTION100
3.74-4.710.25221310.28042414X-RAY DIFFRACTION99.88
4.72-58.40.28461390.20922543X-RAY DIFFRACTION99.81
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)
14.806147907310.40935695858-0.0778965270333.244081078413.718394764083.110552061890.3608406533690.8822448233220.6969115359690.6098016294250.1798042866660.7955730310380.672297341396-0.343216879063-0.9846337772072.184834401010.508496835306-0.1350194674741.22903822940.1771815586491.34361051226-22.688819334434.60280993895.75679133843
28.75869791364-0.744176190751-2.418481972378.105105192883.28984979344.316104866830.3927767811690.6364064002160.0884592311148-0.55663908887-0.2394860230710.132987242158-0.40440458294-0.713383019554-0.0136448991441.44454817530.3654731973380.06532957770791.089304809210.08387174209141.140311771-20.055312235728.965802856712.7089263863
36.742270251621.868498316453.90323392540.8147584788761.813442368052.63219205062-0.2589539553460.6477419960120.244349229268-0.3222638614090.00545643948421-0.22390841340.1330656973420.2026720309340.154770561851.764453570020.3999293270060.3995877997071.019220759990.3070693634831.23451823733.0820843423942.143779052617.9267096574
47.408982865470.1163387133110.6270937013695.671933592880.5284597546053.525114143410.8662492886171.461116457590.11706776601-0.409504023791-0.3092687851210.5865882627360.2956266009170.276515276194-0.29084614811.656605707920.4495944166080.0020999462971.118660768730.1276555057261.272283827595.4517643424348.827274125815.4929587749
58.02580764674-0.3641925887812.967918894725.97125202439-0.08365811147032.85021511394-0.2827282641240.5736796688810.995443170977-0.4210649764460.286835998194-0.872813688449-0.2858897630470.418280034966-0.2369823172621.447229003070.3368345874580.2578992948221.022195757350.0604897648951.2462216289215.273084784652.82549731719.9809065916
68.84184196925-0.692385251884-0.9009975627978.11251111937-3.226285596278.927527349740.201241793654-0.886385639623-0.1183283026290.78809846064-0.05034302928590.838889352368-0.474791232301-0.0941899593766-0.1630703066660.893005186842-0.1009569636390.2112557465761.2321169111-0.234045388971.1451704740915.63601916632.03837537732-2.9072149719
75.257315013183.866256383640.9373196511953.33400167855-4.255473398456.45785585017-0.170670540034-0.25133409973-0.3446636404570.5139291253040.03264540071320.05888210194990.3159699699650.426514193070.04057414448991.22004290540.4064341501540.1184778161960.8615280700130.1103848997881.1260416802811.253106699935.746161804926.4564459209
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'G' and (resid 2 through 38 )GA2 - 381 - 31
22chain 'G' and (resid 39 through 108 )GA39 - 10832 - 91
33chain 'G' and (resid 109 through 159 )GA109 - 15992 - 138
44chain 'G' and (resid 160 through 192 )GA160 - 192139 - 171
55chain 'G' and (resid 193 through 232 )GA193 - 232172 - 211
66chain 'A' and (resid 1 through 126 )AB1 - 1261 - 115
77chain 'A' and (resid 127 through 230 )AB127 - 230116 - 219

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