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- PDB-9u01: De novo TIM barrel with Kemp eliminase activity - KempTIM1 (apo) -

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Basic information

Entry
Database: PDB / ID: 9u01
TitleDe novo TIM barrel with Kemp eliminase activity - KempTIM1 (apo)
ComponentsKempTIM1
KeywordsDE NOVO PROTEIN / Kemp Eliminase / de novo / TIM barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKriegel, M. / Beck, J. / Chica, R.A. / Hocker, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)951375European Union
CitationJournal: Nat.Chem.Biol. / Year: 2026
Title: Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes.
Authors: Beck, J. / Smith, B.J. / Kriegel, M. / Zarifi, N. / Freund, E. / Harsha, A.G. / Hartmann, J. / Chica, R.A. / Hocker, B.
History
DepositionJan 26, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KempTIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9035
Polymers23,6551
Non-polymers2484
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint11 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.170, 66.690, 71.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein KempTIM1


Mass: 23654.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.25→33.35 Å / Num. obs: 54927 / % possible obs: 99.98 % / Redundancy: 12.6 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 1 / Net I/σ(I): 14.09
Reflection shellResolution: 1.25→1.28 Å / Num. unique obs: 3588 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→33.34 Å / SU ML: 0.1408 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.8343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1773 2099 3.82 %
Rwork0.157 52818 -
obs0.1578 54917 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.5 Å2
Refinement stepCycle: LAST / Resolution: 1.25→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 16 185 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071794
X-RAY DIFFRACTIONf_angle_d1.08872435
X-RAY DIFFRACTIONf_chiral_restr0.0831282
X-RAY DIFFRACTIONf_plane_restr0.0126330
X-RAY DIFFRACTIONf_dihedral_angle_d13.8651687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.32631370.29673451X-RAY DIFFRACTION99.94
1.28-1.310.32621380.26173484X-RAY DIFFRACTION100
1.31-1.350.27271380.22623467X-RAY DIFFRACTION100
1.35-1.390.23641380.2113476X-RAY DIFFRACTION99.97
1.39-1.430.22791390.20253484X-RAY DIFFRACTION100
1.43-1.480.2361390.1823495X-RAY DIFFRACTION99.97
1.48-1.540.20381380.15673472X-RAY DIFFRACTION100
1.54-1.610.18611390.14313489X-RAY DIFFRACTION100
1.61-1.70.1471390.1323503X-RAY DIFFRACTION100
1.7-1.80.18641400.13233530X-RAY DIFFRACTION99.97
1.8-1.940.14891400.13453513X-RAY DIFFRACTION100
1.94-2.140.1751400.13333537X-RAY DIFFRACTION100
2.14-2.450.16641420.13043564X-RAY DIFFRACTION100
2.45-3.080.19371430.15783600X-RAY DIFFRACTION99.95
3.08-33.340.15421490.16513753X-RAY DIFFRACTION99.92

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