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- PDB-9tzd: De novo TIM barrel with Kemp eliminase activity - KempTIM1 with b... -

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Basic information

Entry
Database: PDB / ID: 9tzd
TitleDe novo TIM barrel with Kemp eliminase activity - KempTIM1 with bound transition state analogue
ComponentsKempTIM1
KeywordsDE NOVO PROTEIN / Kemp Eliminase / de novo / TIM barrel
Function / homology6-NITROBENZOTRIAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 22, 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)24,1877
Polymers23,6551
Non-polymers5336
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint13 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.220, 67.270, 70.920
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-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: tri-Sodium acetate pH 4.5, 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: 1.2→33.63 Å / Num. obs: 61955 / % possible obs: 99.22 % / Redundancy: 13 % / Biso Wilson estimate: 15.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06834 / Net I/σ(I): 16.97
Reflection shellResolution: 1.2→1.23 Å / Num. unique obs: 4030 / CC1/2: 0.468

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→33.63 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1756 2100 3.39 %
Rwork0.154 59846 -
obs0.1548 61946 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.02 Å2
Refinement stepCycle: LAST / Resolution: 1.2→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 36 191 1875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911819
X-RAY DIFFRACTIONf_angle_d1.18992474
X-RAY DIFFRACTIONf_chiral_restr0.0804280
X-RAY DIFFRACTIONf_plane_restr0.0131333
X-RAY DIFFRACTIONf_dihedral_angle_d13.4319699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.31341370.28693892X-RAY DIFFRACTION98.01
1.23-1.260.28061370.25663899X-RAY DIFFRACTION98.42
1.26-1.290.2811370.22333926X-RAY DIFFRACTION98.31
1.29-1.330.23251380.19373909X-RAY DIFFRACTION98.71
1.33-1.370.19041370.173919X-RAY DIFFRACTION98.49
1.37-1.420.20441390.15733950X-RAY DIFFRACTION99.34
1.42-1.480.19961380.15253948X-RAY DIFFRACTION99.1
1.48-1.550.1841400.14183974X-RAY DIFFRACTION99.35
1.55-1.630.18511380.11453948X-RAY DIFFRACTION99.51
1.63-1.730.14081410.11144018X-RAY DIFFRACTION99.57
1.73-1.860.18371410.1234020X-RAY DIFFRACTION99.86
1.86-2.050.15951410.12864022X-RAY DIFFRACTION99.88
2.05-2.350.15621430.13144049X-RAY DIFFRACTION99.98
2.35-2.960.17011440.15784114X-RAY DIFFRACTION100
2.96-33.630.16621490.1684258X-RAY DIFFRACTION99.77

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