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- PDB-7fh6: Friedel-Crafts alkylation enzyme CylK -

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Basic information

Entry
Database: PDB / ID: 7fh6
TitleFriedel-Crafts alkylation enzyme CylK
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 / CylK
Function and homology information
Biological speciesCylindrospermum licheniforme UTEX B 2014 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsLiu, L. / Wang, H.Q. / 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 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CylK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,19217
Polymers72,6031
Non-polymers58916
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.450, 78.440, 126.560
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

#1: Protein CylK


Mass: 72602.602 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25-28% PEG 3350, Tris buffer, pH 8.0, 0.2-0.4 M magnesium chloride

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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: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→31.84 Å / Num. obs: 85729 / % possible obs: 97.36 % / Redundancy: 11.3 % / Biso Wilson estimate: 13.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05068 / Rpim(I) all: 0.01487 / Rrim(I) all: 0.05289 / Net I/σ(I): 30.45
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.2124 / Mean I/σ(I) obs: 5.32 / Num. unique obs: 6982 / CC1/2: 0.967 / CC star: 0.992 / Rpim(I) all: 0.1013 / Rrim(I) all: 0.2364 / % possible all: 80.61

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Blu-Icedata collection
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→31.84 Å / SU ML: 0.118 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.0085
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1776 4312 5.03 %
Rwork0.1515 81392 -
obs0.1528 85704 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.59 Å2
Refinement stepCycle: LAST / Resolution: 1.55→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 16 603 5641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00595304
X-RAY DIFFRACTIONf_angle_d0.87257237
X-RAY DIFFRACTIONf_chiral_restr0.0585762
X-RAY DIFFRACTIONf_plane_restr0.0062973
X-RAY DIFFRACTIONf_dihedral_angle_d6.3268727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.2930.18271887X-RAY DIFFRACTION68.68
1.57-1.580.22721190.17262206X-RAY DIFFRACTION79.95
1.58-1.60.21751160.16312345X-RAY DIFFRACTION84.89
1.6-1.620.17671330.16762522X-RAY DIFFRACTION91.21
1.62-1.650.20741300.16412590X-RAY DIFFRACTION93.54
1.65-1.670.21131340.15822688X-RAY DIFFRACTION96.74
1.67-1.690.1921400.16112728X-RAY DIFFRACTION98.42
1.69-1.720.17961510.15462727X-RAY DIFFRACTION99.21
1.72-1.740.19481470.15122773X-RAY DIFFRACTION99.76
1.74-1.770.20771520.15972756X-RAY DIFFRACTION100
1.77-1.80.17221570.1482754X-RAY DIFFRACTION99.97
1.8-1.840.19561390.15522786X-RAY DIFFRACTION99.97
1.84-1.870.19211240.15812794X-RAY DIFFRACTION100
1.87-1.910.19821710.16062747X-RAY DIFFRACTION100
1.91-1.950.18961600.15082771X-RAY DIFFRACTION100
1.95-20.17081420.15632761X-RAY DIFFRACTION99.97
2-2.050.20611270.15332792X-RAY DIFFRACTION99.97
2.05-2.10.22541370.14972819X-RAY DIFFRACTION99.97
2.1-2.160.17321610.14632761X-RAY DIFFRACTION100
2.16-2.230.17291400.15572816X-RAY DIFFRACTION100
2.23-2.310.19481350.15312795X-RAY DIFFRACTION100
2.31-2.40.18611480.15482802X-RAY DIFFRACTION99.9
2.4-2.510.17761560.15892779X-RAY DIFFRACTION99.93
2.51-2.650.18511570.16642799X-RAY DIFFRACTION99.97
2.65-2.810.1761500.1632818X-RAY DIFFRACTION100
2.81-3.030.18011440.16162832X-RAY DIFFRACTION99.9
3.03-3.330.1741720.14752816X-RAY DIFFRACTION99.97
3.33-3.820.14711510.13162859X-RAY DIFFRACTION99.97
3.82-4.80.14781510.12322880X-RAY DIFFRACTION99.9
4.81-31.840.16151750.15922989X-RAY DIFFRACTION99.4

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