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- PDB-8vtp: Structure of FabS1CE-EPR-1, a high affinity antibody for the eryt... -

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Basic information

Entry
Database: PDB / ID: 8vtp
TitleStructure of FabS1CE-EPR-1, a high affinity antibody for the erythropoeitin receptor
Components(S1CE VARIANT OF FAB-EPR-1 ...) x 2
KeywordsIMMUNE SYSTEM / proliferation / engineered antibody / high-affinity binding / enhanced crystallization
Function / homologyACETATE ION / AMMONIUM ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSinger, A.U. / Bruce, H.A. / Blazer, L. / Adams, J.J. / Sidhu, S.S.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159640 Canada
Other private United States
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 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: S1CE VARIANT OF FAB-EPR-1 heavy chain
G: S1CE VARIANT OF FAB-EPR-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,72032
Polymers47,1462
Non-polymers1,57530
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-62 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.750, 72.938, 129.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 2 types, 2 molecules AG

#1: Antibody S1CE VARIANT OF FAB-EPR-1 heavy chain


Mass: 24096.021 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 S1CE 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)

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Non-polymers , 7 types, 398 molecules

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


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.35 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Ammonium Acetate, 0.1 M Bis Tris pH 5.5, 17% PEG10K
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: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 10, 2023 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.68→129.58 Å / Num. obs: 72770 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 31.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.02 / Rrim(I) all: 0.064 / Net I/σ(I): 19.3
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.902 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3605 / CC1/2: 0.352 / Rpim(I) all: 0.723 / Rrim(I) all: 2.041 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→64.79 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.4451
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 3046 4.88 %
Rwork0.1747 59315 -
obs0.1757 62361 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.47 Å2
Refinement stepCycle: LAST / Resolution: 1.77→64.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 96 368 3711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763412
X-RAY DIFFRACTIONf_angle_d0.95224609
X-RAY DIFFRACTIONf_chiral_restr0.0627517
X-RAY DIFFRACTIONf_plane_restr0.0098586
X-RAY DIFFRACTIONf_dihedral_angle_d15.71721204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.35461090.31552681X-RAY DIFFRACTION100
1.8-1.830.29971490.27012644X-RAY DIFFRACTION100
1.83-1.860.2781330.24012694X-RAY DIFFRACTION99.93
1.86-1.890.22221320.20562627X-RAY DIFFRACTION99.96
1.89-1.930.24021290.19812673X-RAY DIFFRACTION99.93
1.93-1.970.22311330.19762699X-RAY DIFFRACTION99.96
1.97-2.010.20331180.20542664X-RAY DIFFRACTION99.89
2.01-2.060.22091450.21582671X-RAY DIFFRACTION99.86
2.06-2.110.21381140.20142670X-RAY DIFFRACTION99.86
2.11-2.170.23731410.18792682X-RAY DIFFRACTION99.89
2.17-2.230.21641330.1932675X-RAY DIFFRACTION100
2.23-2.30.25111530.18912667X-RAY DIFFRACTION99.96
2.3-2.380.21221240.1952700X-RAY DIFFRACTION99.96
2.38-2.480.21291600.19682671X-RAY DIFFRACTION99.93
2.48-2.590.22621400.20432692X-RAY DIFFRACTION99.96
2.59-2.730.23791470.18942666X-RAY DIFFRACTION100
2.73-2.90.23571540.18992722X-RAY DIFFRACTION100
2.9-3.120.19161540.18322662X-RAY DIFFRACTION99.58
3.12-3.440.18521500.16922720X-RAY DIFFRACTION100
3.44-3.940.15681510.15732746X-RAY DIFFRACTION99.97
3.94-4.960.16311500.12762762X-RAY DIFFRACTION99.93
4.96-64.790.15651270.162927X-RAY DIFFRACTION99.8
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)
12.25407550158-0.4548092190411.301804104282.204176679660.2252802504772.07798654269-0.1332753157020.0210277142668-0.07229008901590.05245505243560.1322498124780.1123304908470.0692931457113-0.140911837523-0.0007758041598490.194040316823-0.0412965633255-0.01669716401040.2863907685660.02671854330160.2163779307818.9391963676513.77757570913.75671072897
24.012728429750.6861842177931.149062384732.04790950924-0.18207981033.370633475630.231442755201-0.01700767148930.1436757146140.461623968190.176613092833-0.330554584785-0.00105387249680.333585456253-0.4583551059450.2272393724910.007960513253550.03750943006720.1624259260090.03317116283310.17001418496132.019887633425.276693029930.4349003993
31.24387669328-0.315762641197-0.0719373772283.889830625390.4501472252513.445176360390.159378761362-0.1147524150410.04793269766280.369377150347-0.04454714218080.161423265757-0.02248070077870.0775652635324-0.1152913221490.2074490979920.001522815169810.02428595852680.188547406136-0.02286226107430.20863105507527.42571563824.542938351932.7657921326
43.031845478920.1192019353341.025512558653.848839591290.3380361283882.31068207094-0.5144316316090.3042252739130.795306614857-0.2988217088410.2265736808090.0553148289807-0.52063578965-0.08329383535320.2429033655350.39290883801-0.0245498366881-0.2012570444360.3245779955830.1114203298080.4893995114938.3648607646136.19296616253.18750926866
53.41776480683-0.5773401603340.6965271525184.518062135820.1924687079241.92931338453-0.02617796208880.190666961270.0203213759881-0.134188902377-0.061300864526-0.160752713431-0.128059389420.1228686801910.08896805662510.2336755404120.02271838875860.02459127115720.18015592117-0.004653911213130.14700562078736.236612946937.78647981326.3749998726
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 124 )AA1 - 1241 - 113
22chain 'A' and (resid 125 through 159 )AA125 - 159114 - 148
33chain 'A' and (resid 160 through 230 )AA160 - 230149 - 219
44chain 'G' and (resid 1 through 126 )GI1 - 1261 - 106
55chain 'G' and (resid 127 through 232 )GI127 - 232107 - 212

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