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- PDB-9s1t: X-ray crystal structure of a de novo designed six-helix barrel -

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Basic information

Entry
Database: PDB / ID: 9s1t
TitleX-ray crystal structure of a de novo designed six-helix barrel
ComponentsDe novo designed helical barrel - 6H5L
KeywordsDE NOVO PROTEIN / Parametric design / de novo design / helix barrel
Function / homology(2S)-2-hydroxybutanedioic acid / PHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOberdorfer, G. / Elaily, W. / Stoll, D. / Chakatok, M. / Grill, B.
Funding supportEuropean Union, Austria, 2items
OrganizationGrant numberCountry
European Research Council (ERC)802217European Union
Austrian Science FundP30826 Austria
CitationJournal: To Be Published
Title: De novo design of a thermostable helical barrel protein for rapid biocatalytic functionalization
Authors: Elaily, W. / Stoll, D. / Chakatok, M. / Aleotti, M. / Grill, B. / Lechner, H. / Oberdorfer, G.
History
DepositionJul 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed helical barrel - 6H5L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6407
Polymers38,0011
Non-polymers6396
Water52229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.567, 38.600, 59.452
Angle α, β, γ (deg.)101.108, 93.988, 101.919
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein De novo designed helical barrel - 6H5L


Mass: 38000.582 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)
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.1 % / Description: large plate-like shard
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 17.5% PEG 3350, pH = 7.8, 150 mM L-Malic Acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.8→36.91 Å / Num. obs: 14388 / % possible obs: 96.33 % / Redundancy: 1.8 % / Biso Wilson estimate: 63.25 Å2 / CC1/2: 0.994 / CC star: 0.999 / Net I/σ(I): 8.23
Reflection shellResolution: 2.8→3.01 Å / Rmerge(I) obs: 0.11 / Num. unique obs: 2910 / CC1/2: 0.986

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→36.91 Å / SU ML: 0.3171 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 38.3589
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3188 739 10.05 %
Rwork0.2634 6614 -
obs0.269 7353 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.52 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 41 29 2386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00112355
X-RAY DIFFRACTIONf_angle_d0.2733119
X-RAY DIFFRACTIONf_chiral_restr0.0272385
X-RAY DIFFRACTIONf_plane_restr0.0008370
X-RAY DIFFRACTIONf_dihedral_angle_d10.1613985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.010.32481460.25421315X-RAY DIFFRACTION97.01
3.01-3.320.31791490.27261354X-RAY DIFFRACTION97.72
3.32-3.80.34951510.25221342X-RAY DIFFRACTION97.26
3.8-4.780.30641490.2341318X-RAY DIFFRACTION96.51
4.78-36.910.31311440.29931285X-RAY DIFFRACTION93.22

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