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- PDB-7fh7: Friedel-Crafts alkylation enzyme CylK mutant Y37F -

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Basic information

Entry
Database: PDB / ID: 7fh7
TitleFriedel-Crafts alkylation enzyme CylK mutant Y37F
ComponentsCylK
KeywordsBIOSYNTHETIC PROTEIN / cylindrocyclophane / biosynthesis / beta-propeller / calcium-binding / Friedel-Crafts alkylation
Function / homologyBeta-propeller repeat / : / Beta-propeller repeat / Six-bladed beta-propeller, TolB-like / Quinoprotein alcohol dehydrogenase-like superfamily / metal ion binding / Chem-4ON / CylK
Function and homology information
Biological speciesCylindrospermum licheniforme UTEX B 2014 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsWang, H.Q. / Wei, Z. / Xiang, Z.
CitationJournal: ACS Catal. / Year: 2022
Title: Structural Basis for the Friedel-Crafts Alkylation in Cylindrocyclophane Biosynthesis
Authors: Wang, H.Q. / Mou, S.B. / Xiao, W. / Zhou, H. / Hou, X.D. / Wang, S.J. / Wang, Q. / Gao, J. / Wei, Z. / Liu, L. / Xiang, Z.
History
DepositionJul 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CylK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,02526
Polymers73,6061
Non-polymers1,41925
Water12,953719
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.610, 78.370, 127.000
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

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Protein , 1 types, 1 molecules A

#1: Protein CylK


Mass: 73605.883 Da / Num. of mol.: 1 / Mutation: Y37F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cylindrospermum licheniforme UTEX B 2014 (bacteria)
Gene: cylK / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y0K711

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Non-polymers , 5 types, 744 molecules

#2: Chemical ChemComp-4ON / 5-[(2S,7R)-7-fluoranyl-2-methyl-undecyl]benzene-1,3-diol


Mass: 296.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H29FO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-30% PEG 3350, 0.1 M Tris buffer, 0.2-0.3 M magnesium chloride
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.42→30.3 Å / Num. obs: 113330 / % possible obs: 98.78 % / Redundancy: 12.9 % / Biso Wilson estimate: 13.12 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1395 / Rpim(I) all: 0.04049 / Rrim(I) all: 0.1454 / Net I/σ(I): 14.23
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.455 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 11043 / CC1/2: 0.764 / CC star: 0.931 / Rpim(I) all: 0.4061 / Rrim(I) all: 1.512 / % possible all: 97.43

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.19.1_4122refinement
XDSdata reduction
Blu-Icedata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FH6

7fh6


Resolution: 1.42→30.3 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1791 5776 5.1 %
Rwork0.1345 107473 -
obs0.1368 113249 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.84 Å2
Refinement stepCycle: LAST / Resolution: 1.42→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5026 0 65 719 5810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565405
X-RAY DIFFRACTIONf_angle_d0.86097390
X-RAY DIFFRACTIONf_chiral_restr0.084782
X-RAY DIFFRACTIONf_plane_restr0.0053983
X-RAY DIFFRACTIONf_dihedral_angle_d9.2878774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.27562060.22963500X-RAY DIFFRACTION97.42
1.44-1.450.30381930.21563468X-RAY DIFFRACTION97.08
1.45-1.470.21471830.20213490X-RAY DIFFRACTION97.79
1.47-1.490.24551980.19783491X-RAY DIFFRACTION97.67
1.49-1.510.27491940.19293517X-RAY DIFFRACTION97.66
1.51-1.530.27381780.18993514X-RAY DIFFRACTION97.8
1.53-1.550.23591920.17363516X-RAY DIFFRACTION98.1
1.55-1.570.21911850.16733511X-RAY DIFFRACTION97.91
1.57-1.60.21931760.16013563X-RAY DIFFRACTION97.83
1.6-1.630.22231720.15873529X-RAY DIFFRACTION98.56
1.63-1.650.2361690.15143546X-RAY DIFFRACTION98.38
1.65-1.680.2011830.14273571X-RAY DIFFRACTION98.63
1.68-1.720.2061980.13753549X-RAY DIFFRACTION98.63
1.72-1.750.19881810.13423533X-RAY DIFFRACTION98.62
1.75-1.790.22091960.13653583X-RAY DIFFRACTION98.85
1.79-1.830.18821790.13473589X-RAY DIFFRACTION99.03
1.83-1.880.18071990.13533544X-RAY DIFFRACTION99.13
1.88-1.930.16911890.13543582X-RAY DIFFRACTION99.16
1.93-1.980.21261840.13313615X-RAY DIFFRACTION99.35
1.98-2.050.18622080.1293579X-RAY DIFFRACTION99.47
2.05-2.120.1882210.12853571X-RAY DIFFRACTION99.22
2.12-2.210.18681790.1243626X-RAY DIFFRACTION99.56
2.21-2.310.17831980.12653620X-RAY DIFFRACTION99.45
2.31-2.430.1721880.12483643X-RAY DIFFRACTION99.84
2.43-2.580.16352010.1293607X-RAY DIFFRACTION99.63
2.58-2.780.17451940.12953664X-RAY DIFFRACTION99.84
2.78-3.060.17952070.12873665X-RAY DIFFRACTION99.85
3.06-3.50.14461970.11823694X-RAY DIFFRACTION99.95
3.5-4.410.13932090.10773728X-RAY DIFFRACTION99.97
4.41-30.30.1422190.13473865X-RAY DIFFRACTION99.32

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