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- PDB-9fd3: CysG(N-16)-D190N mutant in complex with SAH from Kitasatospora cy... -

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Basic information

Entry
Database: PDB / ID: 9fd3
TitleCysG(N-16)-D190N mutant 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 / homologyMethyltransferase domain 25 / Methyltransferase domain / antibiotic biosynthetic process / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / metal ion binding / S-ADENOSYL-L-HOMOCYSTEINE / SAM-dependent methyltransferase
Function and homology information
Biological speciesKitasatospora cystarginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 16, 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)24,84911
Polymers23,9281
Non-polymers92110
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint4 kcal/mol
Surface area9820 Å2
Unit cell
Length a, b, c (Å)100.690, 100.690, 50.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 23927.934 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
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.24 M Sodium Malonate; 20% PEF 3350

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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: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 50991 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.4
Reflection shellResolution: 1.4→1.5 Å / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9390

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.741 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17612 2547 5 %RANDOM
Rwork0.14976 ---
obs0.15108 48401 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 59 186 1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131761
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151672
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.6492378
X-RAY DIFFRACTIONr_angle_other_deg1.331.5823827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16921.262103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2815281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5041517
X-RAY DIFFRACTIONr_chiral_restr0.0590.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02411
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_it0.9771.765854
X-RAY DIFFRACTIONr_mcbond_other0.9751.765854
X-RAY DIFFRACTIONr_mcangle_it1.272.6551064
X-RAY DIFFRACTIONr_mcangle_other1.272.6551065
X-RAY DIFFRACTIONr_scbond_it1.3452.097907
X-RAY DIFFRACTIONr_scbond_other1.3452.1908
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6643.0191315
X-RAY DIFFRACTIONr_long_range_B_refined2.26422.6271965
X-RAY DIFFRACTIONr_long_range_B_other2.09522.0521933
X-RAY DIFFRACTIONr_rigid_bond_restr0.66333433
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 186 -
Rwork0.281 3525 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: 24.7335 Å / Origin y: -6.6129 Å / Origin z: 8.135 Å
111213212223313233
T0.0133 Å2-0.0116 Å2-0.0028 Å2-0.0139 Å20.0025 Å2--0.0075 Å2
L0.2025 °20.1428 °20.0772 °2-0.1925 °20.1616 °2--0.5154 °2
S-0.0107 Å °0.017 Å °0.0372 Å °-0.0053 Å °0.0083 Å °0.0271 Å °-0.0208 Å °0.0519 Å °0.0024 Å °

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