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- PDB-9c7z: Hallucinated C3 protein assembly HALC3_919 -

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Basic information

Entry
Database: PDB / ID: 9c7z
TitleHallucinated C3 protein assembly HALC3_919
ComponentsHALC3_919
KeywordsDE NOVO PROTEIN / trimer / hallucination / de novo
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRagotte, R. / Bera, A. / Milles, L.F. / Wicky, B.I.M. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Rep / Year: 2025
Title: Designed miniproteins potently inhibit and protect against MERS-CoV.
Authors: Ragotte, R.J. / Tortorici, M.A. / Catanzaro, N.J. / Addetia, A. / Coventry, B. / Froggatt, H.M. / Lee, J. / Stewart, C. / Brown, J.T. / Goreshnik, I. / Sims, J.N. / Milles, L.F. / Wicky, B.I. ...Authors: Ragotte, R.J. / Tortorici, M.A. / Catanzaro, N.J. / Addetia, A. / Coventry, B. / Froggatt, H.M. / Lee, J. / Stewart, C. / Brown, J.T. / Goreshnik, I. / Sims, J.N. / Milles, L.F. / Wicky, B.I.M. / Glogl, M. / Gerben, S. / Kang, A. / Bera, A.K. / Sharkey, W. / Schafer, A. / Harkema, J.R. / Baric, R.S. / Baker, D. / Veesler, D.
History
DepositionJun 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HALC3_919
B: HALC3_919
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3513
Polymers16,1572
Non-polymers1941
Water41423
1
A: HALC3_919
hetero molecules

A: HALC3_919
hetero molecules

A: HALC3_919
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8176
Polymers24,2353
Non-polymers5833
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area5900 Å2
ΔGint-58 kcal/mol
Surface area10420 Å2
MethodPISA
2
B: HALC3_919

B: HALC3_919

B: HALC3_919


Theoretical massNumber of molelcules
Total (without water)24,2353
Polymers24,2353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6620 Å2
ΔGint-55 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.373, 78.373, 78.373
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

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Components

#1: Protein HALC3_919


Mass: 8078.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Sodium citrate tribasic dihydrate pH 4.2, 20% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→55.42 Å / Num. obs: 9601 / % possible obs: 99.89 % / Redundancy: 8.8 % / Biso Wilson estimate: 48.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.988 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1344 / CC1/2: 0.681 / % possible all: 99.41

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→55.42 Å / SU ML: 0.2226 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2386 974 10.14 %
Rwork0.2332 8627 -
obs0.2337 9601 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 8 23 1019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009997
X-RAY DIFFRACTIONf_angle_d1.11411347
X-RAY DIFFRACTIONf_chiral_restr0.046176
X-RAY DIFFRACTIONf_plane_restr0.0065171
X-RAY DIFFRACTIONf_dihedral_angle_d15.6806379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.210.25971310.27041213X-RAY DIFFRACTION99.41
2.21-2.350.23541370.24051209X-RAY DIFFRACTION100
2.35-2.530.21421380.23451227X-RAY DIFFRACTION100
2.53-2.780.29461370.26221216X-RAY DIFFRACTION99.93
2.79-3.190.30071410.28311221X-RAY DIFFRACTION99.93
3.19-4.020.23251390.23281245X-RAY DIFFRACTION100
4.03-55.420.21631510.21081296X-RAY DIFFRACTION99.93

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