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- PDB-9gdj: C-Methyltransferase SgMT from Streptomyces griseoviridis -

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Basic information

Entry
Database: PDB / ID: 9gdj
TitleC-Methyltransferase SgMT from Streptomyces griseoviridis
ComponentsMethyltransferase
KeywordsTRANSFERASE / methyl transfer / pyrroloindole synthesis / Rossmann fold / S-adenosyl methionine
Function / homologyISOPROPYL ALCOHOL / COBALT HEXAMMINE(III) / TRIETHYLENE GLYCOL / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesStreptomyces griseoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsWeiergraeber, O.H. / Haase, M. / Pietruszka, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2025
Title: Characterization of a C-methyltransferase from Streptomyces griseoviridis - crystal structure, mechanism, and substrate scope.
Authors: Haase, M. / Weiergraber, O.H. / David, B. / Pfirmann, E.L. / Paschold, B. / Gohlke, H. / Pietruszka, J.
History
DepositionAug 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,33948
Polymers96,2393
Non-polymers5,10045
Water14,268792
1
A: Methyltransferase
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,28929
Polymers64,1602
Non-polymers3,13027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint1 kcal/mol
Surface area22900 Å2
MethodPISA
2
C: Methyltransferase
hetero molecules

C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,10038
Polymers64,1602
Non-polymers3,94036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8680 Å2
ΔGint12 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.920, 123.920, 126.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-569-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Methyltransferase


Mass: 32079.768 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: GenBank entry WP_189425200.1 / Source: (gene. exp.) Streptomyces griseoviridis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 7 types, 837 molecules

#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: sodium citrate, PEG 4000, 2-propanol, glycerol, hexammine cobalt(III) chloride, S-adenosyl homocysteine, cyclo(Trp-Trp)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.47→37.43 Å / Num. obs: 166186 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 23.75 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.113 / Net I/σ(I): 11.65
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 13.17 % / Mean I/σ(I) obs: 0.78 / Num. unique obs: 12132 / CC1/2: 0.347 / Rrim(I) all: 3.287 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→37.43 Å / SU ML: 0.1766 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1749 3324 2 %
Rwork0.1471 162852 -
obs0.1477 166176 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 1.47→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6213 0 238 792 7243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057331
X-RAY DIFFRACTIONf_angle_d0.7410005
X-RAY DIFFRACTIONf_chiral_restr0.07731059
X-RAY DIFFRACTIONf_plane_restr0.00771343
X-RAY DIFFRACTIONf_dihedral_angle_d13.08532746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.36051360.3086674X-RAY DIFFRACTION99.65
1.49-1.510.32951380.28086733X-RAY DIFFRACTION100
1.51-1.540.28591360.2646671X-RAY DIFFRACTION99.99
1.54-1.560.30491370.25196707X-RAY DIFFRACTION99.99
1.56-1.590.2491370.23276754X-RAY DIFFRACTION100
1.59-1.620.28841360.21936663X-RAY DIFFRACTION100
1.62-1.650.22551380.20326758X-RAY DIFFRACTION99.94
1.65-1.680.25261380.17746735X-RAY DIFFRACTION100
1.68-1.720.22951370.16716730X-RAY DIFFRACTION100
1.72-1.760.21181380.15416735X-RAY DIFFRACTION99.97
1.76-1.80.1961360.1486708X-RAY DIFFRACTION100
1.8-1.850.19341380.14076759X-RAY DIFFRACTION100
1.85-1.910.1941390.13786775X-RAY DIFFRACTION100
1.91-1.970.17221380.13486762X-RAY DIFFRACTION100
1.97-2.040.1511380.12556771X-RAY DIFFRACTION100
2.04-2.120.14751370.12516742X-RAY DIFFRACTION100
2.12-2.220.16621390.12756792X-RAY DIFFRACTION100
2.22-2.330.16751390.13256793X-RAY DIFFRACTION100
2.33-2.480.16711390.13746830X-RAY DIFFRACTION100
2.48-2.670.17741390.14486795X-RAY DIFFRACTION100
2.67-2.940.14541400.14076866X-RAY DIFFRACTION100
2.94-3.360.15341400.14016883X-RAY DIFFRACTION100
3.36-4.240.14541430.13246971X-RAY DIFFRACTION99.99
4.24-37.430.18941480.15347245X-RAY DIFFRACTION99.92

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