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- PDB-7zp5: Crystal structure of designed photoenzyme EnT1.0 -

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Basic information

Entry
Database: PDB / ID: 7zp5
TitleCrystal structure of designed photoenzyme EnT1.0
ComponentsDiisopropyl-fluorophosphatase
KeywordsBIOSYNTHETIC PROTEIN / Designed photoenzyme / [2+2]-cyclase / genetic code expansion / Engineered enzyme
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsHardy, F.J. / Levy, C.
Funding supportEuropean Union, United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council (ERC)757991European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M027023/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/023755/1 United Kingdom
CitationJournal: Nature / Year: 2022
Title: A designed photoenzyme for enantioselective [2+2] cycloadditions.
Authors: Trimble, J.S. / Crawshaw, R. / Hardy, F.J. / Levy, C.W. / Brown, M.J.B. / Fuerst, D.E. / Heyes, D.J. / Obexer, R. / Green, A.P.
History
DepositionApr 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)72,6704
Polymers72,4802
Non-polymers1902
Water8,071448
1
A: Diisopropyl-fluorophosphatase


Theoretical massNumber of molelcules
Total (without water)36,2401
Polymers36,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4303
Polymers36,2401
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.847, 43.397, 81.764
Angle α, β, γ (deg.)90.000, 93.980, 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

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Components

#1: Protein Diisopropyl-fluorophosphatase /


Mass: 36240.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: diisopropyl-fluorophosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-Tris, pH = 5.5, 25% w/v PEG 3350

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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: Feb 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.54→81.57 Å / Num. obs: 89549 / % possible obs: 98.84 % / Redundancy: 6.5 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.05761 / Net I/σ(I): 17.22
Reflection shellResolution: 1.54→1.595 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 0.67 / Num. unique obs: 8084 / CC1/2: 0.801 / CC star: 0.943 / Rpim(I) all: 0.448 / Rrim(I) all: 0.9503 / % possible all: 89.62

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3i1c

3i1c


Resolution: 1.54→81.57 Å / SU ML: 0.2061 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.0419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2231 4542 5.08 %
Rwork0.1959 84914 -
obs0.1968 89456 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.98 Å2
Refinement stepCycle: LAST / Resolution: 1.54→81.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4834 0 10 448 5292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01055050
X-RAY DIFFRACTIONf_angle_d0.99816863
X-RAY DIFFRACTIONf_chiral_restr0.0657717
X-RAY DIFFRACTIONf_plane_restr0.0092906
X-RAY DIFFRACTIONf_dihedral_angle_d9.2437684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.4251250.4092306X-RAY DIFFRACTION82.41
1.56-1.580.37921650.38592563X-RAY DIFFRACTION91.12
1.58-1.60.33531590.36592740X-RAY DIFFRACTION95.17
1.6-1.620.33561550.32982757X-RAY DIFFRACTION98.08
1.62-1.640.3321700.31522790X-RAY DIFFRACTION99.87
1.64-1.660.30661730.29892846X-RAY DIFFRACTION99.64
1.66-1.680.29631640.28932814X-RAY DIFFRACTION99.83
1.68-1.710.34011540.29892820X-RAY DIFFRACTION99.9
1.71-1.730.3111540.2782865X-RAY DIFFRACTION99.87
1.73-1.760.2711390.26962838X-RAY DIFFRACTION99.77
1.76-1.790.28671540.24282846X-RAY DIFFRACTION99.83
1.79-1.830.21441610.22362827X-RAY DIFFRACTION99.93
1.83-1.860.25431500.21892889X-RAY DIFFRACTION99.87
1.86-1.90.21821480.21452831X-RAY DIFFRACTION99.87
1.9-1.940.28921480.20462834X-RAY DIFFRACTION99.93
1.94-1.990.22181240.20512900X-RAY DIFFRACTION100
1.99-2.040.26551510.21032860X-RAY DIFFRACTION100
2.04-2.090.24531430.2122864X-RAY DIFFRACTION100
2.09-2.150.21631150.21152889X-RAY DIFFRACTION100
2.15-2.220.26391630.2022830X-RAY DIFFRACTION100
2.22-2.30.23761510.20422885X-RAY DIFFRACTION99.93
2.3-2.390.22891710.19532836X-RAY DIFFRACTION100
2.39-2.50.22891710.1982849X-RAY DIFFRACTION100
2.5-2.630.25611490.2012886X-RAY DIFFRACTION100
2.63-2.80.22981630.19472871X-RAY DIFFRACTION99.97
2.8-3.010.21041510.19772876X-RAY DIFFRACTION100
3.02-3.320.2191290.18622939X-RAY DIFFRACTION100
3.32-3.80.19551220.16732905X-RAY DIFFRACTION100
3.8-4.790.1621560.13732943X-RAY DIFFRACTION100
4.79-81.570.18061640.17293015X-RAY DIFFRACTION99.91
Refinement TLS params.Method: refined / Origin x: 34.6235960419 Å / Origin y: -12.3873383501 Å / Origin z: 19.7442240728 Å
111213212223313233
T0.335969665378 Å2-0.0237556940638 Å2-0.0416708141867 Å2-0.229075751356 Å2-0.0208049874783 Å2--0.204789395121 Å2
L0.581047156954 °20.0709237526572 °20.0959236252372 °2-0.200179641757 °2-0.105373841206 °2--0.16331335662 °2
S0.00474779940105 Å °0.0650729825163 Å °0.0159423085095 Å °0.0689690820783 Å °-0.0112843684543 Å °-0.038606651334 Å °-0.0627468551946 Å °0.0979100611811 Å °0.00406679353748 Å °
Refinement TLS groupSelection details: all

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