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- PDB-8d06: Hallucinated C3 protein assembly HALC3_104 -

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Basic information

Entry
Database: PDB / ID: 8d06
TitleHallucinated C3 protein assembly HALC3_104
ComponentsHALC3_104
KeywordsDE NOVO PROTEIN / De novo design Hallucination Cyclic Oligomer ProteinMPNN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsRagotte, R.J. / Bera, A.K. / Wicky, B.I.M. / Milles, L.F. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2022
Title: Hallucinating symmetric protein assemblies.
Authors: B I M Wicky / L F Milles / A Courbet / R J Ragotte / J Dauparas / E Kinfu / S Tipps / R D Kibler / M Baek / F DiMaio / X Li / L Carter / A Kang / H Nguyen / A K Bera / D Baker /
Abstract: Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination ...Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination to generate a wide range of symmetric protein homo-oligomers given only a specification of the number of protomers and the protomer length. Crystal structures of seven designs are very similar to the computational models (median root mean square deviation: 0.6 angstroms), as are three cryo-electron microscopy structures of giant 10-nanometer rings with up to 1550 residues and symmetry; all differ considerably from previously solved structures. Our results highlight the rich diversity of new protein structures that can be generated using deep learning and pave the way for the design of increasingly complex components for nanomachines and biomaterials.
History
DepositionMay 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: 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 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HALC3_104
B: HALC3_104
C: HALC3_104
D: HALC3_104
E: HALC3_104
F: HALC3_104
H: HALC3_104
G: HALC3_104
I: HALC3_104
L: HALC3_104
K: HALC3_104
J: HALC3_104


Theoretical massNumber of molelcules
Total (without water)96,84412
Polymers96,84412
Non-polymers00
Water0
1
A: HALC3_104
B: HALC3_104
C: HALC3_104


Theoretical massNumber of molelcules
Total (without water)24,2113
Polymers24,2113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-62 kcal/mol
Surface area9860 Å2
MethodPISA
2
D: HALC3_104
E: HALC3_104
F: HALC3_104


Theoretical massNumber of molelcules
Total (without water)24,2113
Polymers24,2113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-60 kcal/mol
Surface area9610 Å2
MethodPISA
3
H: HALC3_104
G: HALC3_104
I: HALC3_104


Theoretical massNumber of molelcules
Total (without water)24,2113
Polymers24,2113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-62 kcal/mol
Surface area9900 Å2
MethodPISA
4
L: HALC3_104
K: HALC3_104
J: HALC3_104


Theoretical massNumber of molelcules
Total (without water)24,2113
Polymers24,2113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-59 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.496, 107.496, 111.699
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein
HALC3_104


Mass: 8070.304 Da / Num. of mol.: 12
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: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Cesium chloride 0.1 M MES 30% Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97926 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.4→77.45 Å / Num. obs: 17541 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 118.17 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.56
Reflection shellResolution: 3.4→3.522 Å / Mean I/σ(I) obs: 2.61 / Num. unique obs: 1749 / CC1/2: 0.748 / % possible all: 99.43

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Design model

Resolution: 3.4→77.45 Å / SU ML: 0.4909 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 39.983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3086 1005 5.75 %
Rwork0.2838 16483 -
obs0.2852 17488 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 133.44 Å2
Refinement stepCycle: LAST / Resolution: 3.4→77.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 0 0 6344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266390
X-RAY DIFFRACTIONf_angle_d0.52748492
X-RAY DIFFRACTIONf_chiral_restr0.0319994
X-RAY DIFFRACTIONf_plane_restr0.00221038
X-RAY DIFFRACTIONf_dihedral_angle_d19.40382577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.580.37741260.34792363X-RAY DIFFRACTION99.56
3.58-3.80.34921780.32892320X-RAY DIFFRACTION99.92
3.8-4.10.30991380.29162362X-RAY DIFFRACTION99.8
4.1-4.510.27871200.26912372X-RAY DIFFRACTION99.88
4.51-5.160.35741910.30122295X-RAY DIFFRACTION99.44
5.16-6.50.39411130.35332395X-RAY DIFFRACTION99.33
6.5-77.450.25871390.24222376X-RAY DIFFRACTION98.09

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