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- PDB-6xxv: Crystal Structure of a computationally designed Immunogen S2_1.2 ... -

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Basic information

Entry
Database: PDB / ID: 6xxv
TitleCrystal Structure of a computationally designed Immunogen S2_1.2 in complex with its elicited antibody C57
Components
  • Antibody C57, Heavy Chain
  • Antibody C57, Light Chain
  • S2_1.2
KeywordsIMMUNE SYSTEM / epitope scaffold / de novo designed protein / immunogen
Function / homologyRibosome-recycling factor / Topoisomerase I; Chain A, domain 4 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20116418766 Å
AuthorsYang, C. / Sesterhenn, F. / Correia, B.E. / Pojer, F.
Funding support Switzerland, European Union, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation2015/333 Switzerland
European Commission716058European Union
Swiss National Science Foundation310030-163139 Switzerland
CitationJournal: Science / Year: 2020
Title: De novo protein design enables the precise induction of RSV-neutralizing antibodies.
Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. ...Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. / Corthesy, P. / Georgeon, S. / Villard, M. / Richard, C.A. / Descamps, D. / Delgado, T. / Oricchio, E. / Rameix-Welti, M.A. / Mas, V. / Ervin, S. / Eleouet, J.F. / Riffault, S. / Bates, J.T. / Julien, J.P. / Li, Y. / Jardetzky, T. / Krey, T. / Correia, B.E.
History
DepositionJan 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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: Antibody C57, Heavy Chain
B: Antibody C57, Light Chain
C: S2_1.2
D: Antibody C57, Heavy Chain
E: Antibody C57, Light Chain
F: S2_1.2


Theoretical massNumber of molelcules
Total (without water)134,0106
Polymers134,0106
Non-polymers00
Water5,170287
1
A: Antibody C57, Heavy Chain
B: Antibody C57, Light Chain
C: S2_1.2


Theoretical massNumber of molelcules
Total (without water)67,0053
Polymers67,0053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Antibody C57, Heavy Chain
E: Antibody C57, Light Chain
F: S2_1.2


Theoretical massNumber of molelcules
Total (without water)67,0053
Polymers67,0053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)241.019, 66.890, 91.384
Angle α, β, γ (deg.)90.000, 110.811, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Antibody C57, Heavy Chain


Mass: 27005.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody C57, Light Chain


Mass: 25521.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein S2_1.2


Mass: 14478.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium tartrate dibasic, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.97 Å / Num. obs: 67660 / % possible obs: 97.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 46.9217889225 Å2 / Rrim(I) all: 0.053 / Net I/σ(I): 22.59
Reflection shellResolution: 2.2→2.33 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 52096 / Rrim(I) all: 0.779 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JLR

4jlr


Resolution: 2.20116418766→48.97 Å / SU ML: 0.321425444791 / Cross valid method: NONE / σ(F): 1.35000269217 / Phase error: 27.8345679291
RfactorNum. reflection% reflection
Rfree0.244047924956 3830 2.91292410426 %
Rwork0.208535887634 --
obs0.209576207106 67660 97.2155062145 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.5994896265 Å2
Refinement stepCycle: LAST / Resolution: 2.20116418766→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8431 0 0 287 8718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005959902316648634
X-RAY DIFFRACTIONf_angle_d0.80830626634911693
X-RAY DIFFRACTIONf_chiral_restr0.04793830891131295
X-RAY DIFFRACTIONf_plane_restr0.004551293648591501
X-RAY DIFFRACTIONf_dihedral_angle_d16.21304195635237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2012-2.2290.3561791691851270.351550479154305X-RAY DIFFRACTION86.410606356
2.229-2.25841344297X-RAY DIFFRACTION91.2291537986
2.2584-2.28930.4123785704371470.3318863320744519X-RAY DIFFRACTION92.6713008937
2.2893-2.3220.3569903368431230.3104241836894630X-RAY DIFFRACTION94.5494330615
2.322-2.35670.3488431421111400.2916582425614694X-RAY DIFFRACTION96.2948207171
2.3567-2.39350.2854017152431500.2848871561874735X-RAY DIFFRACTION97.4466387393
2.3935-2.43270.3249296139521420.2807624366344652X-RAY DIFFRACTION97.2413793103
2.4327-2.47470.3046091690271460.2671673866434832X-RAY DIFFRACTION97.2265625
2.4747-2.51970.3054049450441370.2614658866754700X-RAY DIFFRACTION97.8159757331
2.5197-2.56810.2903872921111510.2673069784994759X-RAY DIFFRACTION97.5367500993
2.5681-2.62050.2743823377011350.2662853397734763X-RAY DIFFRACTION98.0384307446
2.6205-2.67750.3368772166041480.2684640576434749X-RAY DIFFRACTION97.5498007968
2.6775-2.73980.299665751411450.2697633984654729X-RAY DIFFRACTION98.0881465084
2.7398-2.80830.3017265921510.2452590492024737X-RAY DIFFRACTION98.2512562814
2.8083-2.88420.3127819606941390.2561318050294862X-RAY DIFFRACTION98.6585125271
2.8842-2.96910.2649985985831440.2621584610664811X-RAY DIFFRACTION98.7051792829
2.9691-3.06490.2904722219811400.251190644944812X-RAY DIFFRACTION98.9608313349
3.0649-3.17440.2558172279981370.2500502986574818X-RAY DIFFRACTION98.6855208126
3.1744-3.30150.2660817808271480.2339865094454797X-RAY DIFFRACTION99.0584935897
3.3015-3.45170.3060563701031350.2156809403074824X-RAY DIFFRACTION98.9820359281
3.4517-3.63370.2431338201681420.204439584334796X-RAY DIFFRACTION98.6810551559
3.6337-3.86120.2383464851621520.199133617454752X-RAY DIFFRACTION98.2175045063
3.8612-4.15920.1978773730771390.1758301836974840X-RAY DIFFRACTION98.848520945
4.1592-4.57750.1859561215361500.1496177204044793X-RAY DIFFRACTION99.0978348035
4.5775-5.23920.1958537763681450.1443626263344850X-RAY DIFFRACTION99.4029850746
5.2392-6.59830.1814837965621430.174300862614814X-RAY DIFFRACTION98.9618686365
6.5983-48.970.2010752439181400.1615515455984783X-RAY DIFFRACTION98.4796959392

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