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- PDB-9g0k: CysG(N-16) in complex with SAH (metal free, cocrystallization in ... -

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Basic information

Entry
Database: PDB / ID: 9g0k
TitleCysG(N-16) in complex with SAH (metal free, cocrystallization in presence of EDTA) 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: 2 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
DepositionJul 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7516
Polymers47,8582
Non-polymers8934
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-10 kcal/mol
Surface area17480 Å2
Unit cell
Length a, b, c (Å)99.610, 103.120, 49.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 23928.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora cystarginea (bacteria) / Gene: cysG / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W6R556
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M LiCl, 0.1 M TRIS, 20% PEG 8000 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 34551 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4670 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 16.378 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.588 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26115 1726 5 %RANDOM
Rwork0.21397 ---
obs0.21633 32778 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.743 Å2
Baniso -1Baniso -2Baniso -3
1--3.35 Å20 Å20 Å2
2--7.95 Å2-0 Å2
3----4.6 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 60 17 3427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133480
X-RAY DIFFRACTIONr_bond_other_d0.010.0153270
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.6414728
X-RAY DIFFRACTIONr_angle_other_deg1.4751.5847494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.215424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87421.262206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.315562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.921534
X-RAY DIFFRACTIONr_chiral_restr0.0760.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023984
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02818
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_it9.1233.4891708
X-RAY DIFFRACTIONr_mcbond_other9.1163.4891708
X-RAY DIFFRACTIONr_mcangle_it10.7385.2522128
X-RAY DIFFRACTIONr_mcangle_other10.7385.2522129
X-RAY DIFFRACTIONr_scbond_it11.6724.0011772
X-RAY DIFFRACTIONr_scbond_other11.6694.0021773
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.1035.8242601
X-RAY DIFFRACTIONr_long_range_B_refined12.46741.4663744
X-RAY DIFFRACTIONr_long_range_B_other12.45541.4573743
X-RAY DIFFRACTIONr_rigid_bond_restr32.00136750
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6558 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 127 -
Rwork0.38 2407 -
obs--99.41 %

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