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- PDB-9fcl: CysG(N-16) in complex with SAM from Kitasatospora cystarginea -

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Basic information

Entry
Database: PDB / ID: 9fcl
TitleCysG(N-16) in complex with SAM from Kitasatospora cystarginea
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / Natural Product Biosynthesis / Enzyme Mechanism / Metal Ion interaction / Molecular Docking / Structure Function Relationships
Function / homology
Function and homology information


antibiotic biosynthetic process / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / SAM-dependent methyltransferase
Similarity search - Component
Biological speciesKitasatospora cystarginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKuttenlochner, W. / Beller, P. / Kaysser, L. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309 - 325871075 Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Deciphering the SAM- and metal-dependent mechanism of O-methyltransferases in cystargolide and belactosin biosynthesis: A structure-activity relationship study.
Authors: Kuttenlochner, W. / Beller, P. / Kaysser, L. / Groll, M.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,13814
Polymers23,9291
Non-polymers1,20913
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint13 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.540, 101.540, 49.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SAM-dependent methyltransferase


Mass: 23928.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora cystarginea (bacteria) / Gene: cysG / Plasmid: pETDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W6R556

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Non-polymers , 5 types, 101 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.1 M HEPES, 0.2 M NaCl, 26% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 26735 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.1
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4054 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.55 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19884 1336 5 %RANDOM
Rwork0.15703 ---
obs0.15917 25391 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å20 Å2
2--0.79 Å20 Å2
3----1.59 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 78 88 1834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131770
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151692
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.652382
X-RAY DIFFRACTIONr_angle_other_deg1.2321.5823873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70521.262103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03415280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0751517
X-RAY DIFFRACTIONr_chiral_restr0.0540.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02408
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.982.763850
X-RAY DIFFRACTIONr_mcbond_other1.9782.763850
X-RAY DIFFRACTIONr_mcangle_it2.4754.1481059
X-RAY DIFFRACTIONr_mcangle_other2.4744.1491060
X-RAY DIFFRACTIONr_scbond_it2.7593.311920
X-RAY DIFFRACTIONr_scbond_other2.7613.313921
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.284.7491324
X-RAY DIFFRACTIONr_long_range_B_refined3.63633.9531915
X-RAY DIFFRACTIONr_long_range_B_other3.58433.8521910
X-RAY DIFFRACTIONr_rigid_bond_restr1.01233462
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 97 -
Rwork0.239 1840 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 25.3057 Å / Origin y: -7.0853 Å / Origin z: 8.0815 Å
111213212223313233
T0.0123 Å2-0.0129 Å2-0.006 Å2-0.0172 Å20.0044 Å2--0.0065 Å2
L0.2458 °20.2653 °20.1505 °2-0.3045 °20.2338 °2--0.7964 °2
S-0.0196 Å °0.0054 Å °0.0367 Å °-0.01 Å °-0.0012 Å °0.0362 Å °-0.0253 Å °0.0635 Å °0.0209 Å °

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