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- PDB-9fcs: CysG(N-16)-H122N mutant in complex with SAH from Kitasatospora cy... -

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Basic information

Entry
Database: PDB / ID: 9fcs
TitleCysG(N-16)-H122N 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: 1.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8278
Polymers47,8102
Non-polymers1,0176
Water4,666259
1
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3513
Polymers23,9051
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4755
Polymers23,9051
Non-polymers5714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.630, 100.800, 49.840
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: 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES; 0.2 M NaCl, 25% 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: Jun 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 67193 / % possible obs: 99.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 11037 / % 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: 1.6→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.328 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18586 3357 5 %RANDOM
Rwork0.15371 ---
obs0.1553 63771 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.25 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: 1 / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 68 259 3673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153280
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.6434724
X-RAY DIFFRACTIONr_angle_other_deg1.2671.5847514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0365424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6921.359206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23215562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.331534
X-RAY DIFFRACTIONr_chiral_restr0.0520.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02818
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_it1.0311.9641708
X-RAY DIFFRACTIONr_mcbond_other1.031.9641708
X-RAY DIFFRACTIONr_mcangle_it1.4562.9512128
X-RAY DIFFRACTIONr_mcangle_other1.4562.9512129
X-RAY DIFFRACTIONr_scbond_it1.3682.3051772
X-RAY DIFFRACTIONr_scbond_other1.3682.3061773
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.73.3462597
X-RAY DIFFRACTIONr_long_range_B_refined2.6524.6163894
X-RAY DIFFRACTIONr_long_range_B_other2.5624.3083854
X-RAY DIFFRACTIONr_rigid_bond_restr0.63436760
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 243 -
Rwork0.218 4620 -
obs--99.77 %
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)
10.23020.1596-0.14050.1809-0.03010.5720.0009-0.0017-0.0250.0106-0.0068-0.0352-0.04490.01380.00590.009-0.0046-0.00390.0040.00250.0075-6.73724.8947-8.0921
20.18720.1511-0.01960.2085-0.11850.555-0.01010.0074-0.0349-0.00560.0005-0.02410.0083-0.04570.00960.0039-0.00420.00260.0087-0.00320.007-24.826.76128.0755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 901
2X-RAY DIFFRACTION2B17 - 901

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