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- PDB-9fug: Crystal structure of SNAr1.3 (K39A) in complex with 2,4-dinitroio... -

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Basic information

Entry
Database: PDB / ID: 9fug
TitleCrystal structure of SNAr1.3 (K39A) in complex with 2,4-dinitroiodobenzene
ComponentsSNAr1.3 (K39A)
KeywordsBIOSYNTHETIC PROTEIN / SNArase
Function / homology: / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsRoberts, G.R. / Leys, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/W014483/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/023755/1 United Kingdom
CitationJournal: Nature / Year: 2025
Title: Engineered enzymes for enantioselective nucleophilic aromatic substitutions.
Authors: Lister, T.M. / Roberts, G.W. / Hossack, E.J. / Zhao, F. / Burke, A.J. / Johannissen, L.O. / Hardy, F.J. / Millman, A.A.V. / Leys, D. / Larrosa, I. / Green, A.P.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: 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

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Assembly

Deposited unit
A: SNAr1.3 (K39A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0144
Polymers27,5791
Non-polymers4363
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-8 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.364, 70.364, 119.519
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

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Components

#1: Protein SNAr1.3 (K39A)


Mass: 27578.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-A1IGD / 2,4-dinitroiodobenzene / 1-iodanyl-2,4-dinitro-benzene


Mass: 294.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3IN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic dihydrate, 20% 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: Apr 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.71→54.29 Å / Num. obs: 37752 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 35.48 Å2 / CC1/2: 1 / Net I/σ(I): 13.8
Reflection shellResolution: 1.71→1.75 Å / Num. unique obs: 1857 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→42.67 Å / SU ML: 0.2693 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.0756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 1959 5.23 %
Rwork0.2038 35526 -
obs0.2058 37485 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.28 Å2
Refinement stepCycle: LAST / Resolution: 1.71→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 21 201 2064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582040
X-RAY DIFFRACTIONf_angle_d0.62222762
X-RAY DIFFRACTIONf_chiral_restr0.0455294
X-RAY DIFFRACTIONf_plane_restr0.0051359
X-RAY DIFFRACTIONf_dihedral_angle_d16.6252810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.40541290.39582330X-RAY DIFFRACTION92.3
1.75-1.80.38391430.37662506X-RAY DIFFRACTION99.81
1.8-1.850.36721190.38052531X-RAY DIFFRACTION99.96
1.85-1.910.37461600.32252467X-RAY DIFFRACTION99.81
1.91-1.980.31011440.27382522X-RAY DIFFRACTION100
1.98-2.060.31221280.2332554X-RAY DIFFRACTION99.96
2.06-2.150.24671450.22672487X-RAY DIFFRACTION100
2.15-2.270.25441570.21072542X-RAY DIFFRACTION100
2.27-2.410.30081250.22782537X-RAY DIFFRACTION99.96
2.41-2.60.25751250.19732585X-RAY DIFFRACTION100
2.6-2.860.23661240.2232564X-RAY DIFFRACTION99.96
2.86-3.270.21821570.2062563X-RAY DIFFRACTION100
3.27-4.120.23361490.1732614X-RAY DIFFRACTION100
4.12-42.670.20521540.16922724X-RAY DIFFRACTION99.93

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