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- PDB-7fh8: Friedel-Crafts alkylation enzyme CylK mutant H391A -

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Basic information

Entry
Database: PDB / ID: 7fh8
TitleFriedel-Crafts alkylation enzyme CylK mutant H391A
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-4PJ / CylK
Function and homology information
Biological speciesCylindrospermum licheniforme UTEX B 2014 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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)74,97826
Polymers73,5551
Non-polymers1,42325
Water14,394799
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.280, 78.460, 126.290
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: 73554.812 Da / Num. of mol.: 1 / Mutation: H391A
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, 824 molecules

#2: Chemical ChemComp-4PJ / 2-[(5S,10S)-11-[3,5-bis(oxidanyl)phenyl]-10-methyl-undecan-5-yl]-5-[(2S,7R)-7-fluoranyl-2-methyl-undecyl]benzene-1,3-diol


Mass: 572.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H57FO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / 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.: 799 / 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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-30% PEG 3350, 0.1 Mm 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: BL17U / 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: 1.32→23.9 Å / Num. obs: 140902 / % possible obs: 99.96 % / Redundancy: 13 % / Biso Wilson estimate: 13.59 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0798 / Rpim(I) all: 0.02285 / Rrim(I) all: 0.08305 / Net I/σ(I): 21.38
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.182 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 13934 / CC1/2: 0.769 / CC star: 0.933 / Rpim(I) all: 0.3462 / Rrim(I) all: 1.233 / % possible all: 99.99

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Processing

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

7fh6


Resolution: 1.32→23.9 Å / SU ML: 0.1004 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.8448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1538 7108 5.05 %
Rwork0.1208 133779 -
obs0.1225 140887 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.2 Å2
Refinement stepCycle: LAST / Resolution: 1.32→23.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 65 799 5886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00555507
X-RAY DIFFRACTIONf_angle_d0.88087548
X-RAY DIFFRACTIONf_chiral_restr0.0882798
X-RAY DIFFRACTIONf_plane_restr0.00581010
X-RAY DIFFRACTIONf_dihedral_angle_d11.9834798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.330.22232110.19484424X-RAY DIFFRACTION99.98
1.34-1.350.24192460.19044387X-RAY DIFFRACTION100
1.35-1.370.22032350.17654430X-RAY DIFFRACTION99.98
1.37-1.380.22652640.17964372X-RAY DIFFRACTION100
1.38-1.40.1852260.1684456X-RAY DIFFRACTION100
1.4-1.420.2042290.15684389X-RAY DIFFRACTION99.98
1.42-1.440.2122410.14954424X-RAY DIFFRACTION100
1.44-1.460.21172290.14724389X-RAY DIFFRACTION99.98
1.46-1.490.18092230.14094460X-RAY DIFFRACTION100
1.49-1.510.18622560.12814421X-RAY DIFFRACTION99.98
1.51-1.540.162400.11564410X-RAY DIFFRACTION99.98
1.54-1.560.1492290.10644436X-RAY DIFFRACTION99.98
1.56-1.60.14982350.10884421X-RAY DIFFRACTION100
1.6-1.630.14162200.10794430X-RAY DIFFRACTION99.96
1.63-1.660.15312410.10774435X-RAY DIFFRACTION100
1.66-1.70.1632340.10364420X-RAY DIFFRACTION99.98
1.7-1.740.14032180.10274480X-RAY DIFFRACTION100
1.74-1.790.14852310.11364459X-RAY DIFFRACTION99.98
1.79-1.840.14822480.114424X-RAY DIFFRACTION99.96
1.84-1.90.12912310.10494454X-RAY DIFFRACTION100
1.9-1.970.13972440.10324445X-RAY DIFFRACTION100
1.97-2.050.13632550.1054443X-RAY DIFFRACTION100
2.05-2.140.14472130.10464503X-RAY DIFFRACTION100
2.14-2.260.14912620.10924457X-RAY DIFFRACTION99.96
2.26-2.40.15122370.11324508X-RAY DIFFRACTION100
2.4-2.580.14762440.12054461X-RAY DIFFRACTION100
2.58-2.840.16112370.12814525X-RAY DIFFRACTION100
2.84-3.250.16552610.12564521X-RAY DIFFRACTION100
3.25-4.090.12792510.11074595X-RAY DIFFRACTION100
4.1-23.90.14922170.13444800X-RAY DIFFRACTION99.92

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