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- PDB-9fcy: CysG(N-16)-R21K mutant in complex with SAH from Kitasatospora cys... -

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Basic information

Entry
Database: PDB / ID: 9fcy
TitleCysG(N-16)-R21K 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 / ADENINE / 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 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
C: SAM-dependent methyltransferase
D: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,30412
Polymers95,6044
Non-polymers7018
Water6,359353
1
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0763
Polymers23,9011
Non-polymers1752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0763
Polymers23,9011
Non-polymers1752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0763
Polymers23,9011
Non-polymers1752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0763
Polymers23,9011
Non-polymers1752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.970, 106.170, 99.070
Angle α, β, γ (deg.)90.00, 90.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SAM-dependent methyltransferase


Mass: 23900.906 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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.1 M HEPES; 0.2 M NaCl; 20% PEG 4000

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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: Jul 2, 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: 87037 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.3
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 12753 / % 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: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.072 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19613 4351 5 %RANDOM
Rwork0.14868 ---
obs0.15105 82670 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.55 Å2
2--0.4 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 44 353 7035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136818
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156427
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.6349261
X-RAY DIFFRACTIONr_angle_other_deg1.2511.58314717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.385842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96821.421401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.664151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6791564
X-RAY DIFFRACTIONr_chiral_restr0.0560.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021610
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_it2.1323.0513380
X-RAY DIFFRACTIONr_mcbond_other2.1313.053378
X-RAY DIFFRACTIONr_mcangle_it2.8144.5794218
X-RAY DIFFRACTIONr_mcangle_other2.8144.5794218
X-RAY DIFFRACTIONr_scbond_it2.4373.5753438
X-RAY DIFFRACTIONr_scbond_other2.4353.5743438
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1515.2015044
X-RAY DIFFRACTIONr_long_range_B_refined3.90937.5137542
X-RAY DIFFRACTIONr_long_range_B_other3.84137.347504
X-RAY DIFFRACTIONr_rigid_bond_restr1.022313245
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
Rfree0.284 321 -
Rwork0.237 6107 -
obs--99.55 %
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)
10.4967-0.1490.17660.1256-0.20680.36550.0010.0840.04670.0032-0.0252-0.0194-0.00640.0130.02420.00190.00330.00270.04470.01760.01317.5801-28.2809-16.8566
20.94750.09870.18410.28660.06620.18780.06130.0116-0.10790.0114-0.0134-0.01440.0393-0.002-0.04790.0120.0044-0.01830.008-0.00840.032716.1654.67590.8934
30.9267-0.0982-0.16360.29380.07670.18060.0511-0.01170.1129-0.0044-0.0079-0.0144-0.035-0.0044-0.04310.0134-0.00370.02060.0083-0.00780.035916.3639-10.7872-50.3756
40.51260.1574-0.16650.1013-0.18750.40970.0033-0.0869-0.0476-0.001-0.0248-0.01950.00510.01040.02150.0012-0.0030.00160.04130.01910.017917.743922.2117-32.6106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 902
2X-RAY DIFFRACTION2B17 - 902
3X-RAY DIFFRACTION3C18 - 902
4X-RAY DIFFRACTION4D17 - 902

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