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- PDB-9fcu: CysG(N-16)-H121A mutant in complex with SAH from Kitasatospora cy... -

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Basic information

Entry
Database: PDB / ID: 9fcu
TitleCysG(N-16)-H121A 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 / 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: 1.85 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,3988
Polymers95,8604
Non-polymers1,5384
Water7,044391
1
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3492
Polymers23,9651
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3492
Polymers23,9651
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3492
Polymers23,9651
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3492
Polymers23,9651
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.780, 49.710, 102.510
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
SAM-dependent methyltransferase


Mass: 23964.994 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES; 0.02 M MgCl2; 22% Sodium Polyacrylate 5100

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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: Jun 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 85811 / % possible obs: 98.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 12473 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.812 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23145 4290 5 %RANDOM
Rwork0.19216 ---
obs0.19336 81503 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.328 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-0.78 Å2
2---0.71 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6680 0 104 391 7175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136924
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156516
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.6419416
X-RAY DIFFRACTIONr_angle_other_deg1.1791.58414932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1621.275408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.704151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4261568
X-RAY DIFFRACTIONr_chiral_restr0.050.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021628
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_it0.9861.9723416
X-RAY DIFFRACTIONr_mcbond_other0.9861.9723416
X-RAY DIFFRACTIONr_mcangle_it1.3552.9544256
X-RAY DIFFRACTIONr_mcangle_other1.3542.9544257
X-RAY DIFFRACTIONr_scbond_it1.1542.2653508
X-RAY DIFFRACTIONr_scbond_other1.1542.2653508
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5233.3045161
X-RAY DIFFRACTIONr_long_range_B_refined2.29623.8667534
X-RAY DIFFRACTIONr_long_range_B_other2.1823.6917479
X-RAY DIFFRACTIONr_rigid_bond_restr0.539313440
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 317 -
Rwork0.266 6031 -
obs--99.02 %
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)
10.22430.02010.1040.57150.11910.2546-0.00680.02150.0052-0.03080.01210.0289-0.00570.0041-0.00530.0052-0.0044-0.00530.00670.00610.007425.7469-8.29786.8313
20.19450.14350.11150.62680.06460.1610.00180.0157-0.00230.06560.0131-0.03260.01730.0152-0.01490.01220.0025-0.00810.0027-0.00330.013543.20987.896325.571
30.21360.0078-0.14540.6067-0.06710.1805-0.00860.02040.0039-0.03580.0161-0.02830.0099-0.0122-0.00750.0092-0.00690.00850.0068-0.00610.009524.54328.167758.0759
40.2774-0.1532-0.10470.63740.07440.1396-0.0021-0.01340.0064-0.06240.0241-0.0453-0.01610.01-0.0220.0162-0.00410.01690.0027-0.00440.02-7.1759-8.020125.6917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 901
2X-RAY DIFFRACTION2B17 - 901
3X-RAY DIFFRACTION3C17 - 901
4X-RAY DIFFRACTION4D17 - 901

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