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- PDB-9fcq: CysG(N-16)-H122A mutant in complex with SAH from Kitasatospora cy... -

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Basic information

Entry
Database: PDB / ID: 9fcq
TitleCysG(N-16)-H122A 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 / 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-ADENOSYL-L-HOMOCYSTEINE / SAM-dependent methyltransferase
Similarity search - Component
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 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)24,85012
Polymers23,8621
Non-polymers98811
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint4 kcal/mol
Surface area9780 Å2
Unit cell
Length a, b, c (Å)100.010, 100.010, 49.720
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: 23861.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora cystarginea (bacteria) / Gene: cysG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W6R556

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Non-polymers , 6 types, 151 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 140 / 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: 2.61 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES; 0.2 M NaCl; 25% PEG 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: 50023 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.6
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9221 / % possible all: 100

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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: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.148 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19747 2499 5 %RANDOM
Rwork0.1686 ---
obs0.17005 47483 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.866 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å20 Å2
2--0.17 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 63 141 1874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131757
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151674
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.6492369
X-RAY DIFFRACTIONr_angle_other_deg1.2761.5833833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67821.275102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64815280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3761517
X-RAY DIFFRACTIONr_chiral_restr0.0510.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
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_it0.8521.792853
X-RAY DIFFRACTIONr_mcbond_other0.851.791853
X-RAY DIFFRACTIONr_mcangle_it1.0772.6941061
X-RAY DIFFRACTIONr_mcangle_other1.0762.6941062
X-RAY DIFFRACTIONr_scbond_it1.052.088903
X-RAY DIFFRACTIONr_scbond_other1.052.09904
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3053.0211308
X-RAY DIFFRACTIONr_long_range_B_refined1.8722.7241981
X-RAY DIFFRACTIONr_long_range_B_other1.76822.4111958
X-RAY DIFFRACTIONr_rigid_bond_restr0.50133430
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
Rfree0.279 182 -
Rwork0.282 3449 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: 24.6374 Å / Origin y: -6.6877 Å / Origin z: 8.0824 Å
111213212223313233
T0.0126 Å2-0.0002 Å2-0 Å2-0.0128 Å20.0009 Å2--0.0005 Å2
L0.0296 °20.0206 °20.0023 °2-0.0286 °20.0067 °2--0.0765 °2
S-0.0001 Å °0.0013 Å °0.0019 Å °-0.0014 Å °-0.0015 Å °0.0032 Å °-0.0018 Å °0.0041 Å °0.0016 Å °

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