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- PDB-9fcd: CysG(N-16) in complex with SAH from Kitasatospora cystarginea -

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Basic information

Entry
Database: PDB / ID: 9fcd
TitleCysG(N-16) in complex with SAH 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
CARBONATE ION / S-ADENOSYL-L-HOMOCYSTEINE / SAM-dependent methyltransferase
Similarity search - Component
Biological speciesKitasatospora cystarginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)25,20613
Polymers23,9291
Non-polymers1,27712
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-29 kcal/mol
Surface area9840 Å2
Unit cell
Length a, b, c (Å)101.190, 101.190, 49.790
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 , 7 types, 133 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.0 M (NH4)2SO4; 0.1 M HEPES; 2% PEG 400

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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: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 40256 / % possible obs: 96 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.3
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 6976 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.273 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17149 2012 5 %RANDOM
Rwork0.14594 ---
obs0.14721 38239 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0 Å20 Å2
2---0.88 Å20 Å2
3---1.76 Å2
Refinement stepCycle: 1 / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 79 121 1875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131779
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151672
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.6452404
X-RAY DIFFRACTIONr_angle_other_deg1.3441.5823832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14521.262103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36815281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3161517
X-RAY DIFFRACTIONr_chiral_restr0.0560.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
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_it1.2961.715854
X-RAY DIFFRACTIONr_mcbond_other1.2931.715854
X-RAY DIFFRACTIONr_mcangle_it1.82.581064
X-RAY DIFFRACTIONr_mcangle_other1.7992.581065
X-RAY DIFFRACTIONr_scbond_it1.7052.124923
X-RAY DIFFRACTIONr_scbond_other1.7042.126924
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1283.0591341
X-RAY DIFFRACTIONr_long_range_B_refined2.87422.1371967
X-RAY DIFFRACTIONr_long_range_B_other2.80121.9751955
X-RAY DIFFRACTIONr_rigid_bond_restr0.90333449
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 145 -
Rwork0.22 2752 -
obs--95.86 %
Refinement TLS params.Method: refined / Origin x: 6.9043 Å / Origin y: 25.0965 Å / Origin z: 8.1188 Å
111213212223313233
T0.0209 Å20.0003 Å2-0.0003 Å2-0.0206 Å20.0002 Å2--0.0001 Å2
L0.0228 °20.0025 °20.0115 °2-0.0073 °20.015 °2--0.0337 °2
S-0.0001 Å °0.001 Å °-0.0013 Å °-0.0018 Å °0.0001 Å °0.0002 Å °0.0005 Å °-0.0003 Å °0 Å °

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