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- PDB-9eno: Crystal structure of ComplemEnT1.4 (CEnT1.4), an engineered photo... -

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Basic information

Entry
Database: PDB / ID: 9eno
TitleCrystal structure of ComplemEnT1.4 (CEnT1.4), an engineered photoenzyme for selective [2+2]-cycloadditions
ComponentsDiisopropyl-fluorophosphatase
KeywordsBIOSYNTHETIC PROTEIN / photoenzyme / [2+2]-cyclase / artificial enzyme
Function / homology
Function and homology information


diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / calcium ion binding
Similarity search - Function
: / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Diisopropyl-fluorophosphatase
Similarity search - Component
Biological speciesLoligo vulgaris (squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsHardy, F.J. / Crawshaw, R.C. / Green, A.P.
Funding supportEuropean Union, United Kingdom, France, 6items
OrganizationGrant numberCountry
European Research Council (ERC)757991European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M027023/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M027023/1 United Kingdom
Human Frontier Science Program (HFSP)RGP0004/2022 France
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S507969/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/W524347/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Photosensitizer Repositioning Affords an Enantiocomplementary Enzyme for [2 + 2]-Cycloadditions.
Authors: Sun, C. / Kohn, A.R. / Smithson, R. / Hardy, F.J. / Trimble, J.S. / Cao, Y. / Johannissen, L.O. / Hay, S. / Crawshaw, R. / Green, A.P.
History
DepositionMar 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diisopropyl-fluorophosphatase
B: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6587
Polymers73,1712
Non-polymers4875
Water8,089449
1
A: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7103
Polymers36,5851
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9484
Polymers36,5851
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.970, 73.917, 74.870
Angle α, β, γ (deg.)90.000, 92.850, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Diisopropyl-fluorophosphatase / DFPase


Mass: 36585.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo vulgaris (squid) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIG4, EC: 3.1.8.2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0 M ammonium sulphate, 0.2 M sodium chloride, 0.1 M sodium cacodylate
Temp details: humidified cabinet

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.73→51.91 Å / Num. obs: 59053 / % possible obs: 98.97 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.07 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1659 / Net I/σ(I): 6.98
Reflection shellResolution: 1.73→1.792 Å / Rmerge(I) obs: 2.152 / Mean I/σ(I) obs: 0.41 / Num. unique obs: 5851 / CC1/2: 0.459 / % possible all: 92.25

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Processing

Software
NameVersionClassification
PDB-REDOrefinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→51.91 Å / SU ML: 0.2353 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.2614
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2259 2081 3.55 %
Rwork0.1812 56480 -
obs0.1828 58561 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.49 Å2
Refinement stepCycle: LAST / Resolution: 1.73→51.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 32 449 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675010
X-RAY DIFFRACTIONf_angle_d0.96326791
X-RAY DIFFRACTIONf_chiral_restr0.0589715
X-RAY DIFFRACTIONf_plane_restr0.0107897
X-RAY DIFFRACTIONf_dihedral_angle_d11.1591696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.31381270.31033313X-RAY DIFFRACTION88.07
1.77-1.810.34351120.29873762X-RAY DIFFRACTION98.35
1.81-1.860.35271100.28593779X-RAY DIFFRACTION99.01
1.86-1.920.29071440.27943771X-RAY DIFFRACTION99.16
1.92-1.980.27411270.25023758X-RAY DIFFRACTION99.64
1.98-2.050.24441310.22523803X-RAY DIFFRACTION99.8
2.05-2.130.29641640.20313767X-RAY DIFFRACTION99.87
2.13-2.230.21771570.19313769X-RAY DIFFRACTION99.57
2.23-2.350.25051720.18643762X-RAY DIFFRACTION99.85
2.35-2.490.24231700.17673773X-RAY DIFFRACTION99.95
2.49-2.690.28051540.17753801X-RAY DIFFRACTION99.97
2.69-2.960.23411170.17553836X-RAY DIFFRACTION100
2.96-3.380.21261040.16053853X-RAY DIFFRACTION99.97
3.38-4.260.16751360.13983845X-RAY DIFFRACTION100
4.26-51.910.17911560.15493888X-RAY DIFFRACTION99.9

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