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- PDB-9r7f: De novo designed enzyme for the Morita-Baylis-Hillman reaction (MBH48) -

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Basic information

Entry
Database: PDB / ID: 9r7f
TitleDe novo designed enzyme for the Morita-Baylis-Hillman reaction (MBH48)
ComponentsMBH48
KeywordsDE NOVO PROTEIN / Morita-Baylis-Hillman enzyme
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsTripp, A. / Fischer, C. / Moser, M. / Oberdorfer, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Nature / Year: 2026
Title: Computational enzyme design by catalytic motif scaffolding.
Authors: Braun, M. / Tripp, A. / Chakatok, M. / Kaltenbrunner, S. / Fischer, C. / Stoll, D. / Bijelic, A. / Elaily, W. / Totaro, M.G. / Moser, M. / Hoch, S.Y. / Lechner, H. / Rossi, F. / Aleotti, M. ...Authors: Braun, M. / Tripp, A. / Chakatok, M. / Kaltenbrunner, S. / Fischer, C. / Stoll, D. / Bijelic, A. / Elaily, W. / Totaro, M.G. / Moser, M. / Hoch, S.Y. / Lechner, H. / Rossi, F. / Aleotti, M. / Hall, M. / Oberdorfer, G.
History
DepositionMay 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 7, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MBH48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,34012
Polymers23,3191
Non-polymers1,02111
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-22 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.056, 76.056, 59.638
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-488-

HOH

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Components

#1: Protein MBH48


Mass: 23319.416 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.93→44.21 Å / Num. obs: 14602 / % possible obs: 98.24 % / Redundancy: 20.7 % / Biso Wilson estimate: 41.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.145 / Net I/σ(I): 13
Reflection shellResolution: 1.93→2.08 Å / Rmerge(I) obs: 2.226 / Num. unique obs: 2697 / CC1/2: 0.756

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→44.21 Å / SU ML: 0.3402 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.9529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2517 749 5.13 %
Rwork0.2014 13853 -
obs0.204 14602 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.32 Å2
Refinement stepCycle: LAST / Resolution: 1.93→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 64 88 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591572
X-RAY DIFFRACTIONf_angle_d0.77852118
X-RAY DIFFRACTIONf_chiral_restr0.0423238
X-RAY DIFFRACTIONf_plane_restr0.0078272
X-RAY DIFFRACTIONf_dihedral_angle_d19.5236575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.080.49941410.38732556X-RAY DIFFRACTION91.49
2.08-2.290.30321490.24792791X-RAY DIFFRACTION99.69
2.29-2.620.3191500.26992832X-RAY DIFFRACTION100
2.62-3.30.24711660.22062802X-RAY DIFFRACTION100
3.3-44.210.21211430.15692872X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -9.01819122782 Å / Origin y: -26.2436952885 Å / Origin z: -1.08445358952 Å
111213212223313233
T0.311890059258 Å20.0806643515895 Å2-0.0152858881207 Å2-0.312025402529 Å20.00266767039063 Å2--0.322460727115 Å2
L3.6477578254 °20.39198768594 °2-0.0738287825128 °2-0.646214791779 °2-0.0299130653569 °2--1.44214528031 °2
S-0.0240055511123 Å °0.105639342858 Å °0.402577077247 Å °0.0166705148364 Å °0.0154690043525 Å °0.0119878315691 Å °-0.251621346751 Å °0.000881832702125 Å °0.0072542151137 Å °
Refinement TLS groupSelection details: all

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