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- PDB-7roo: Crystal structure of Friedel-Crafts alkylating enzyme CylK from C... -

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Basic information

Entry
Database: PDB / ID: 7roo
TitleCrystal structure of Friedel-Crafts alkylating enzyme CylK from Cylindospermum licheniforme with bromide
ComponentsCylK
KeywordsTRANSFERASE / beta-propeller / beta-roll / halide / Friedel-Crafts / cylindrocyclophane
Function / homologyBeta-propeller repeat / : / Beta-propeller repeat / Six-bladed beta-propeller, TolB-like / Quinoprotein alcohol dehydrogenase-like superfamily / metal ion binding / BROMIDE ION / CylK
Function and homology information
Biological speciesCylindrospermum licheniforme UTEX B 2014 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 1.2Oct 18, 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

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Assembly

Deposited unit
A: CylK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,04925
Polymers74,8221
Non-polymers1,22624
Water7,260403
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)93.470, 138.656, 99.511
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-823-

HOH

21A-879-

HOH

31A-895-

HOH

41A-1083-

HOH

51A-1158-

HOH

61A-1181-

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 , 6 types, 427 molecules

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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
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. CylK crystals were soaked in 2 M sodium malonate with 500 mM NaBr for up to 1 min

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 98866 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.99 / Net I/σ(I): 23.3
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.14 / Num. unique obs: 4856 / CC1/2: 0.843

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RON

7ron


Resolution: 1.52→46.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.904 / SU B: 1.317 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 4649 5 %RANDOM
Rwork0.1693 ---
obs0.1708 89122 94.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.77 Å2 / Biso mean: 15.772 Å2 / Biso min: 4.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.52→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 45 403 5426
Biso mean--23.94 23.81 -
Num. residues----645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135129
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174409
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.6366962
X-RAY DIFFRACTIONr_angle_other_deg1.5541.58310269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2535649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66124.945275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31815776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5411514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021096
LS refinement shellResolution: 1.521→1.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 218 -
Rwork0.238 4340 -
all-4558 -
obs--63.03 %

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