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- PDB-6ywd: De novo designed protein 4H_01 in complex with Mota antibody -

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Basic information

Entry
Database: PDB / ID: 6ywd
TitleDe novo designed protein 4H_01 in complex with Mota antibody
Components
  • Antibody Mota, Heavy Chain
  • Antibody Mota, Light Chain
  • De novo designed protein 4H_01
KeywordsDE NOVO PROTEIN / De novo designed protein
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody Mota, Heavy Chain
B: Antibody Mota, Light Chain
C: De novo designed protein 4H_01


Theoretical massNumber of molelcules
Total (without water)59,3583
Polymers59,3583
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-35 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.710, 143.710, 90.223
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 Antibody Mota, Heavy Chain


Mass: 25033.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody Mota, Light Chain


Mass: 23899.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein De novo designed protein 4H_01


Mass: 10424.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 4.53 Å3/Da / Density % sol: 72.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M bicine pH 9.3, 22% v/v PEG Smear Broad

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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: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→47.1 Å / Num. obs: 757244 / % possible obs: 99.8 % / Redundancy: 14.7 % / Biso Wilson estimate: 76.37 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.6
Reflection shellResolution: 2.8→2.96 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 117130 / CC1/2: 0.56 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JLR

4jlr


Resolution: 3.2→47.04 Å / SU ML: 0.4546 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.983 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2472 3372 9.87 %
Rwork0.2064 30786 -
obs0.2104 34158 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.88 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 0 0 3906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00364000
X-RAY DIFFRACTIONf_angle_d0.79715444
X-RAY DIFFRACTIONf_chiral_restr0.0491624
X-RAY DIFFRACTIONf_plane_restr0.0044687
X-RAY DIFFRACTIONf_dihedral_angle_d4.65642394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.250.44671290.37511223X-RAY DIFFRACTION96.71
3.25-3.290.39771330.34131260X-RAY DIFFRACTION99.57
3.29-3.350.33081550.33211335X-RAY DIFFRACTION99.27
3.35-3.40.39211310.30751265X-RAY DIFFRACTION99.64
3.4-3.460.31631470.28411288X-RAY DIFFRACTION98.9
3.46-3.520.33311410.26941249X-RAY DIFFRACTION98.86
3.52-3.590.35521420.25841289X-RAY DIFFRACTION98.76
3.59-3.660.27591380.25251253X-RAY DIFFRACTION98.03
3.66-3.740.26211410.25091241X-RAY DIFFRACTION98.71
3.74-3.830.30451500.22411322X-RAY DIFFRACTION99.73
3.83-3.920.2511300.21991286X-RAY DIFFRACTION99.79
3.92-4.030.24561400.22831279X-RAY DIFFRACTION99.86
4.03-4.150.25481500.21631286X-RAY DIFFRACTION99.93
4.15-4.280.21051390.16791301X-RAY DIFFRACTION99.59
4.28-4.440.19391430.16791293X-RAY DIFFRACTION100
4.44-4.610.23261420.16571292X-RAY DIFFRACTION100
4.61-4.820.17641350.16691286X-RAY DIFFRACTION99.86
4.82-5.080.19661440.15621283X-RAY DIFFRACTION99.93
5.08-5.390.21541300.17161311X-RAY DIFFRACTION99.72
5.39-5.810.24971440.18561269X-RAY DIFFRACTION99.51
5.81-6.390.2471450.1991301X-RAY DIFFRACTION99.52
6.39-7.320.29211370.19881294X-RAY DIFFRACTION99.79
7.32-9.210.17291350.1611291X-RAY DIFFRACTION99.79
9.21-47.040.19981510.17621289X-RAY DIFFRACTION99.86

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