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- PDB-9fcx: CysG(N-16)-H121N mutant in complex with SAH from Kitasatospora cy... -

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Basic information

Entry
Database: PDB / ID: 9fcx
TitleCysG(N-16)-H121N 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: / Methyltransferase domain 25 / Methyltransferase domain / biosynthetic process / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / SAM-dependent methyltransferase
Function and homology information
Biological speciesKitasatospora cystarginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,44818
Polymers47,8102
Non-polymers1,63816
Water3,747208
1
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4134
Polymers23,9051
Non-polymers5093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,03414
Polymers23,9051
Non-polymers1,12913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.870, 99.870, 98.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-1006-

HOH

21B-1094-

HOH

31B-1098-

HOH

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 23904.877 Da / Num. of mol.: 2
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.: 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.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES; 0.02 M MgCl2; 22% Sodium Polyacrylate 5100
PH range: 7.5

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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: 1.8→30 Å / Num. obs: 45416 / % possible obs: 97.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6847 / % 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: 1.8→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.312 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20388 2270 5 %RANDOM
Rwork0.15906 ---
obs0.16125 43132 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.502 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 108 208 3674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133522
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153338
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.6484760
X-RAY DIFFRACTIONr_angle_other_deg1.1681.5837644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36221.359206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12515564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4641534
X-RAY DIFFRACTIONr_chiral_restr0.0440.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023998
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02820
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_it0.9712.4821716
X-RAY DIFFRACTIONr_mcbond_other0.972.4821716
X-RAY DIFFRACTIONr_mcangle_it1.3913.7262138
X-RAY DIFFRACTIONr_mcangle_other1.3913.7262139
X-RAY DIFFRACTIONr_scbond_it1.1692.8371806
X-RAY DIFFRACTIONr_scbond_other1.1692.8391807
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5654.1262623
X-RAY DIFFRACTIONr_long_range_B_refined2.24630.4263887
X-RAY DIFFRACTIONr_long_range_B_other2.22630.2153860
X-RAY DIFFRACTIONr_rigid_bond_restr0.45436860
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 170 -
Rwork0.231 3236 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.15160.1793-0.05610.35560.11550.7113-0.0135-0.01010.0211-0.007-0.00720.008-0.01790.04830.02070.0044-0.0012-0.00670.00890.0020.010424.0615-6.5688-16.5527
20.23680.16630.05430.23290.11310.53680.0031-0.0040.00830.0071-0.03770.03330.014-0.04350.03460.0006-0.00220.00130.0116-0.00860.00785.7283-24.1769-32.8879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 901
2X-RAY DIFFRACTION2B16 - 901

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