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- PDB-9szu: Cerium(III)-bound de novo photoredox enzyme (PLZ2.3) -

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Basic information

Entry
Database: PDB / ID: 9szu
TitleCerium(III)-bound de novo photoredox enzyme (PLZ2.3)
ComponentsPLZ2.3
KeywordsDE NOVO PROTEIN / artificial metalloenzyme / cerium / photoenzyme
Function / homologyCERIUM (III) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLeiss-Maier, F. / Behringer, J. / Mustafa, G. / Heider, A. / Muehlhofer, R. / Klein, A.S. / Groll, M. / Zeymer, C.
Funding supportEuropean Union, Germany, 3items
OrganizationGrant numberCountry
European Research Council (ERC)101039592European Union
German Research Foundation (DFG)453748800 Germany
German Research Foundation (DFG)439143547 Germany
CitationJournal: Chem Sci / Year: 2026
Title: Computational redesign and directed evolution of a lanthanide-dependent photoredox enzyme for enantioselective diol cleavage.
Authors: Leiss-Maier, F. / Behringer, J. / Mustafa, G. / Heider, A. / Muhlhofer, R. / Klein, A.S. / Groll, M. / Zeymer, C.
History
DepositionOct 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 3, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLZ2.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7495
Polymers36,5401
Non-polymers2094
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-46 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.190, 93.190, 51.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein PLZ2.3


Mass: 36540.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29 / Details (production host): Kanamycin / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / Variant (production host): (DE3)
#2: Chemical ChemComp-CE / CERIUM (III) ION


Mass: 140.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ce
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Sodium acetate pH 4.6 2.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0596 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0596 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 24843 / % possible obs: 95.7 % / Redundancy: 2.83 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3286 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 15.367 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.898 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24063 1242 5 %RANDOM
Rwork0.17915 ---
obs0.18229 23592 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.577 Å2
Baniso -1Baniso -2Baniso -3
1-3.43 Å20 Å20 Å2
2--3.43 Å20 Å2
3----6.87 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 4 81 2567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132503
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152572
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.6243387
X-RAY DIFFRACTIONr_angle_other_deg1.1831.5795870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30421.727139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14215460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5361525
X-RAY DIFFRACTIONr_chiral_restr0.0550.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022820
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7064.6121286
X-RAY DIFFRACTIONr_mcbond_other3.6954.611285
X-RAY DIFFRACTIONr_mcangle_it4.8376.9181604
X-RAY DIFFRACTIONr_mcangle_other4.8356.9191605
X-RAY DIFFRACTIONr_scbond_it3.9495.1991217
X-RAY DIFFRACTIONr_scbond_other3.9475.21218
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0937.6151784
X-RAY DIFFRACTIONr_long_range_B_refined6.16155.3732578
X-RAY DIFFRACTIONr_long_range_B_other6.03355.2652567
X-RAY DIFFRACTIONr_rigid_bond_restr1.19535075
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 92 -
Rwork0.266 1746 -
obs--97.51 %
Refinement TLS params.Method: refined / Origin x: 1.4561 Å / Origin y: -28.398 Å / Origin z: 0.2655 Å
111213212223313233
T0.0047 Å20.001 Å20.0003 Å2-0.0006 Å2-0.0001 Å2--0.105 Å2
L0.0436 °20.0166 °2-0.0444 °2-0.1839 °20.0442 °2--0.1017 °2
S-0.0062 Å °0.0024 Å °-0.0017 Å °-0.0006 Å °0.0033 Å °0.0017 Å °0.0185 Å °0.0026 Å °0.0028 Å °

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