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- PDB-7ron: Crystal structure of the Friedel-Crafts alkylating enzyme CylK fr... -

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Basic information

Entry
Database: PDB / ID: 7ron
TitleCrystal structure of the Friedel-Crafts alkylating enzyme CylK from Cylindospermum licheniforme
ComponentsCylK
KeywordsTRANSFERASE / beta-propeller / beta-roll / calcium-dependent / alkylation / cylindrocyclophane
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: 1.68 Å
AuthorsRuskoski, T.B. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2022
Title: Structural basis for an unprecedented enzymatic alkylation in cylindrocyclophane biosynthesis.
Authors: Braffman, N.R. / Ruskoski, T.B. / Davis, K.M. / Glasser, N.R. / Johnson, C. / Okafor, C.D. / Boal, A.K. / Balskus, E.P.
History
DepositionJul 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 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)75,90624
Polymers74,8221
Non-polymers1,08423
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.667, 138.613, 99.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-992-

HOH

21A-1204-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CylK


Mass: 74822.188 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 BL21(DE3) (bacteria) / References: UniProt: A0A1Y0K711

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Non-polymers , 5 types, 362 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Prior to crystallization trials, purified CylK protein in storage buffer (20 mM HEPES pH 7.8, 50 mM NaCl, 10 mM MgCl2, 10 mM CaCl2, 10% glycerol) was combined with 5-undecylbenzene-1,3-diol ...Details: Prior to crystallization trials, purified CylK protein in storage buffer (20 mM HEPES pH 7.8, 50 mM NaCl, 10 mM MgCl2, 10 mM CaCl2, 10% glycerol) was combined with 5-undecylbenzene-1,3-diol (UDR), a substrate analog dissolved in protein storage buffer containing 22% DMSO. The final protein solution contained 10 mg/mL CylK and 1.66 mM UDR. Crystals of undecylresorcinol-bound CylK were obtained by using the hanging drop vapor diffusion method in 2 uL drops mixed in 1:1 ratio with a precipitant solution of 1.8 M sodium malonate, pH 7.0. Crystals formed within about 1 week at room temperature

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 73688 / % possible obs: 99.8 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.026 / Rrim(I) all: 0.101 / Χ2: 0.936 / Net I/σ(I): 7.3 / Num. measured all: 1088178
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.68-1.7114.31.27936770.780.3461.3260.79299.3
1.71-1.7414.51.06436130.8540.2851.1020.79599.4
1.74-1.7714.60.91336260.880.2440.9460.81499.6
1.77-1.8114.60.76236440.9060.2040.7890.84499.6
1.81-1.8514.60.62836330.9380.1680.650.86899.6
1.85-1.8914.70.50736540.9590.1350.5250.88599.8
1.89-1.9414.70.41736570.9730.1110.4310.91399.8
1.94-1.9914.70.34336610.980.0920.3550.9499.8
1.99-2.0514.70.28736170.9860.0770.2970.99599.9
2.05-2.1214.80.23536830.990.0630.2441.04199.9
2.12-2.1914.80.19536650.9930.0520.2021.024100
2.19-2.2814.90.16736950.9940.0440.1730.997100
2.28-2.38150.14536530.9950.0390.150.986100
2.38-2.5115.10.12636950.9970.0330.130.975100
2.51-2.6715.10.10836990.9970.0280.1111.029100
2.67-2.8715.10.08936880.9980.0240.0921.129100
2.87-3.1615.10.06337180.9990.0170.0661.126100
3.16-3.6215.10.04137420.9990.0110.0420.936100
3.62-4.5614.80.032375310.0090.0330.823100
4.56-5014.30.03239150.9990.0090.0330.78399.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→42.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.179 / WRfactor Rwork: 0.1523 / FOM work R set: 0.8759 / SU B: 3.607 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0896 / SU Rfree: 0.0907 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 3627 5 %RANDOM
Rwork0.1556 ---
obs0.1573 68476 97.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.87 Å2 / Biso mean: 17.173 Å2 / Biso min: 5.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å20 Å2
2---0.26 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.68→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4882 0 50 339 5271
Biso mean--29.48 25.81 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0135046
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174354
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.6366845
X-RAY DIFFRACTIONr_angle_other_deg1.5911.58310140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3935640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65525.056269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54315768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6831513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021072
LS refinement shellResolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 189 -
Rwork0.228 4180 -
all-4369 -
obs--80.49 %
Refinement TLS params.Method: refined / Origin x: 22.531 Å / Origin y: 50.705 Å / Origin z: 32.529 Å
111213212223313233
T0.01 Å20.0022 Å2-0.0001 Å2-0.0134 Å20.0009 Å2--0.0032 Å2
L0.2336 °2-0.1643 °20.0126 °2-0.3218 °2-0.0551 °2--0.2416 °2
S-0.0206 Å °0.0176 Å °-0.0139 Å °0.0395 Å °0.0152 Å °0.0224 Å °-0.0184 Å °0.0352 Å °0.0054 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 662
2X-RAY DIFFRACTION1A801 - 809

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