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- PDB-6ywc: De novo designed protein 4E1H_95 in complex with 101F antibody -

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Basic information

Entry
Database: PDB / ID: 6ywc
TitleDe novo designed protein 4E1H_95 in complex with 101F antibody
Components
  • Antibody 101F, Heavy Chain
  • Antibody 101F, light chain
  • De novo design 4E1H_95
KeywordsDE NOVO PROTEIN / De novo designed protein
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsYang, C. / Sesterhenn, F. / Pojer, F. / Correia, B.E.
Funding support Switzerland, European Union, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation2015/333 Switzerland
European Commission716058European Union
Swiss National Science Foundation310030-163139 Switzerland
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Bottom-up de novo design of functional proteins with complex structural features.
Authors: Yang, C. / Sesterhenn, F. / Bonet, J. / van Aalen, E.A. / Scheller, L. / Abriata, L.A. / Cramer, J.T. / Wen, X. / Rosset, S. / Georgeon, S. / Jardetzky, T. / Krey, T. / Fussenegger, M. / ...Authors: Yang, C. / Sesterhenn, F. / Bonet, J. / van Aalen, E.A. / Scheller, L. / Abriata, L.A. / Cramer, J.T. / Wen, X. / Rosset, S. / Georgeon, S. / Jardetzky, T. / Krey, T. / Fussenegger, M. / Merkx, M. / Correia, B.E.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody 101F, Heavy Chain
B: Antibody 101F, light chain
C: De novo design 4E1H_95
D: Antibody 101F, Heavy Chain
E: Antibody 101F, light chain
F: De novo design 4E1H_95


Theoretical massNumber of molelcules
Total (without water)121,4506
Polymers121,4506
Non-polymers00
Water27015
1
A: Antibody 101F, Heavy Chain
B: Antibody 101F, light chain
C: De novo design 4E1H_95


Theoretical massNumber of molelcules
Total (without water)60,7253
Polymers60,7253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Antibody 101F, Heavy Chain
E: Antibody 101F, light chain
F: De novo design 4E1H_95


Theoretical massNumber of molelcules
Total (without water)60,7253
Polymers60,7253
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.146, 65.417, 128.525
Angle α, β, γ (deg.)90.000, 119.352, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'B' and resid 11 through 227)B13 - 232
221(chain 'E' and resid 11 through 227)E13 - 232
132chain 'A'A11 - 226
242chain 'D'D11 - 226
153chain 'C'C2 - 58
263chain 'F'F2 - 58

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Antibody 101F, Heavy Chain


Mass: 26391.598 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 101F, light chain


Mass: 26018.912 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 De novo design 4E1H_95


Mass: 8314.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 5.8, 0.1 M ammonium sulfate, 16% w/v PEG 4000, 20% v/v glycerol

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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: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→49.5 Å / Num. obs: 71869 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 52.53 Å2 / CC1/2: 0.987 / Net I/σ(I): 7.7
Reflection shellResolution: 2.67→2.84 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 11512 / CC1/2: 0.398 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O41

3o41


Resolution: 2.85→49.45 Å / SU ML: 0.4202 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.4489 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2475 3777 6.44 %
Rwork0.2121 54893 -
obs0.2144 58670 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.69 Å2
Refinement stepCycle: LAST / Resolution: 2.85→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 0 15 7650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00457825
X-RAY DIFFRACTIONf_angle_d0.912210640
X-RAY DIFFRACTIONf_chiral_restr0.0521196
X-RAY DIFFRACTIONf_plane_restr0.00521353
X-RAY DIFFRACTIONf_dihedral_angle_d7.54964650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.890.40491290.33421896X-RAY DIFFRACTION93.27
2.89-2.920.30911360.30512040X-RAY DIFFRACTION96.2
2.92-2.960.34891410.30442044X-RAY DIFFRACTION98.51
2.96-3.010.3051400.27422081X-RAY DIFFRACTION98.84
3.01-3.050.36561400.29251994X-RAY DIFFRACTION98.11
3.05-3.10.32071400.27172062X-RAY DIFFRACTION98.44
3.1-3.150.28871430.25342047X-RAY DIFFRACTION98.43
3.15-3.20.33431460.25662071X-RAY DIFFRACTION98.93
3.2-3.260.3051430.25972057X-RAY DIFFRACTION98.48
3.26-3.320.28151420.24132077X-RAY DIFFRACTION98.19
3.32-3.390.29691370.24031988X-RAY DIFFRACTION98.52
3.39-3.470.27821410.23342065X-RAY DIFFRACTION98.31
3.47-3.550.25651390.23132025X-RAY DIFFRACTION97.87
3.55-3.640.26081410.21662054X-RAY DIFFRACTION96.31
3.64-3.730.2531370.21811956X-RAY DIFFRACTION95.14
3.73-3.840.25561410.20782052X-RAY DIFFRACTION97.73
3.84-3.970.25591390.19831985X-RAY DIFFRACTION98.2
3.97-4.110.26361430.19742057X-RAY DIFFRACTION97.26
4.11-4.270.21121380.18442007X-RAY DIFFRACTION96.23
4.27-4.470.19431360.17061995X-RAY DIFFRACTION96.08
4.47-4.70.19421380.16862019X-RAY DIFFRACTION98.22
4.7-50.18661390.17382092X-RAY DIFFRACTION98.63
5-5.380.24561400.18252059X-RAY DIFFRACTION99.05
5.38-5.920.23851400.1942038X-RAY DIFFRACTION98.82
5.92-6.780.23041480.20742021X-RAY DIFFRACTION97
6.78-8.530.19521390.19512074X-RAY DIFFRACTION98.88
8.53-49.450.18491410.18872037X-RAY DIFFRACTION97.93

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