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- PDB-9qdp: De novo designed enzyme for Morita-Baylis-Hillman reaction MBH2 -

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Basic information

Entry
Database: PDB / ID: 9qdp
TitleDe novo designed enzyme for Morita-Baylis-Hillman reaction MBH2
ComponentsDe novo designed enzyme for Morita-Baylis-Hillman reaction MBH2
KeywordsDE NOVO PROTEIN / Morita-Baylis-Hillman Enzyme
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsTripp, A. / Stoll, D. / Oberdorfer, G. / Fischer, C. / Kaltenbrunner, S.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP30826 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
DepositionMar 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed enzyme for Morita-Baylis-Hillman reaction MBH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4647
Polymers23,1991
Non-polymers2656
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-45 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.775, 51.881, 72.606
Angle α, β, γ (deg.)90.000, 112.273, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

21A-604-

HOH

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Components

#1: Protein De novo designed enzyme for Morita-Baylis-Hillman reaction MBH2


Mass: 23198.838 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Ammonium acetate, Bis-Tris, Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 1.17→36.75 Å / Num. obs: 70627 / % possible obs: 96.77 % / Redundancy: 3.1 % / Biso Wilson estimate: 11.64 Å2 / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 9.83
Reflection shellResolution: 1.17→1.19 Å / Num. unique obs: 2675 / CC1/2: 0.407 / CC star: 0.761 / % possible all: 93.17

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.17→36.75 Å / SU ML: 0.116 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.0904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.164 3202 5.02 %
Rwork0.134 60627 -
obs0.1355 63829 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.87 Å2
Refinement stepCycle: LAST / Resolution: 1.17→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 15 420 1953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481639
X-RAY DIFFRACTIONf_angle_d0.74882237
X-RAY DIFFRACTIONf_chiral_restr0.0449251
X-RAY DIFFRACTIONf_plane_restr0.0077310
X-RAY DIFFRACTIONf_dihedral_angle_d12.6648595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.190.30371140.26142602X-RAY DIFFRACTION95.7
1.19-1.210.26061180.23552645X-RAY DIFFRACTION96.27
1.21-1.230.26121660.21792513X-RAY DIFFRACTION95.85
1.23-1.250.21951380.19152646X-RAY DIFFRACTION95.87
1.25-1.270.21011360.17732581X-RAY DIFFRACTION96.66
1.27-1.290.20471410.17042607X-RAY DIFFRACTION96.18
1.29-1.320.19111220.16492646X-RAY DIFFRACTION96.92
1.32-1.350.21631270.16452625X-RAY DIFFRACTION96.87
1.35-1.380.18861280.14682662X-RAY DIFFRACTION97.11
1.38-1.420.16361250.13092616X-RAY DIFFRACTION97.16
1.42-1.450.151330.11582628X-RAY DIFFRACTION96.78
1.45-1.50.13261690.10042622X-RAY DIFFRACTION96.91
1.5-1.540.13261280.09622642X-RAY DIFFRACTION97.57
1.54-1.60.12351430.09812691X-RAY DIFFRACTION98.27
1.6-1.660.12351390.10482629X-RAY DIFFRACTION97.57
1.66-1.740.1531730.1082441X-RAY DIFFRACTION91.49
1.74-1.830.15341480.10742484X-RAY DIFFRACTION91.42
1.83-1.950.1331450.11212678X-RAY DIFFRACTION99.33
1.95-2.10.12981280.11052719X-RAY DIFFRACTION99.44
2.1-2.310.13881300.10562730X-RAY DIFFRACTION99.76
2.31-2.640.14591470.12132727X-RAY DIFFRACTION99.65
2.64-3.330.16881830.13522707X-RAY DIFFRACTION99.55
3.33-36.750.20971210.17242786X-RAY DIFFRACTION98.51

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