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- PDB-9icz: C-Methyltransferase SeMT from Saccharopolyspora erythraea -

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Basic information

Entry
Database: PDB / ID: 9icz
TitleC-Methyltransferase SeMT from Saccharopolyspora erythraea
ComponentsS-adenosylmethionine (SAM)-dependent methyltransferase
KeywordsTRANSFERASE / methyl transfer / Rossmann fold / S-adenosyl methionine
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Unknown ligand / S-adenosylmethionine (SAM)-dependent methyltransferase
Function and homology information
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsWeiergraeber, O.H. / Haase, M. / Pietruszka, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2025
Title: Re-engineering a transferase scaffold for indole C3 methylation in diketopiperazines.
Authors: Haase, M. / Weiergraber, O.H. / Pietruszka, J.
History
DepositionFeb 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine (SAM)-dependent methyltransferase
B: S-adenosylmethionine (SAM)-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,68617
Polymers62,4522
Non-polymers2,23415
Water11,854658
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-93 kcal/mol
Surface area24130 Å2
Unit cell
Length a, b, c (Å)152.960, 212.990, 48.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-703-

HOH

21B-459-

HOH

31B-491-

HOH

41B-704-

HOH

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Components

#1: Protein S-adenosylmethionine (SAM)-dependent methyltransferase


Mass: 31225.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sample sequence has C-terminus is ...GVLEHHHHHH / Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: SACE_3471 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4FFC0
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O
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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: sodium citrate, Tris-HCl, lithium sulfate, ammonium sulfate, sodium chloride, dimethylsulfoxide, S-adenosyl homocysteine, 1,6-diaminohexane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Feb 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.58→62.12 Å / Num. obs: 106524 / % possible obs: 98.4 % / Redundancy: 4.22 % / Biso Wilson estimate: 29.66 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.059 / Net I/σ(I): 11.38
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 0.64 / Num. unique obs: 7866 / CC1/2: 0.306 / Rrim(I) all: 2.184 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→53.25 Å / SU ML: 0.2759 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1929 3194 3 %
Rwork0.173 103247 -
obs0.1736 106441 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.93 Å2
Refinement stepCycle: LAST / Resolution: 1.58→53.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 85 658 4995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065260
X-RAY DIFFRACTIONf_angle_d0.767248
X-RAY DIFFRACTIONf_chiral_restr0.0522758
X-RAY DIFFRACTIONf_plane_restr0.0074981
X-RAY DIFFRACTIONf_dihedral_angle_d12.86831989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.44831370.51084433X-RAY DIFFRACTION98.11
1.6-1.630.47551380.46444445X-RAY DIFFRACTION98.84
1.63-1.660.42541390.43364499X-RAY DIFFRACTION99.34
1.66-1.680.36851390.38024484X-RAY DIFFRACTION99.38
1.68-1.710.31561390.3284480X-RAY DIFFRACTION99.21
1.71-1.750.32671390.28774503X-RAY DIFFRACTION99.51
1.75-1.780.27691390.24934488X-RAY DIFFRACTION99.21
1.78-1.820.24431380.22334483X-RAY DIFFRACTION99.5
1.82-1.860.2361390.20584524X-RAY DIFFRACTION99.07
1.86-1.910.23121390.19074463X-RAY DIFFRACTION99.22
1.91-1.960.20591380.19594478X-RAY DIFFRACTION98.78
1.96-2.020.24471390.20214504X-RAY DIFFRACTION99.02
2.02-2.090.20391410.16524540X-RAY DIFFRACTION99.49
2.09-2.160.19391390.15624485X-RAY DIFFRACTION99.29
2.16-2.250.21761390.16334493X-RAY DIFFRACTION98.97
2.25-2.350.18471390.16144522X-RAY DIFFRACTION98.92
2.35-2.470.20151400.16554514X-RAY DIFFRACTION98.48
2.47-2.630.19751390.18074484X-RAY DIFFRACTION97.7
2.63-2.830.21791370.17744432X-RAY DIFFRACTION96.41
2.83-3.120.2011360.16924410X-RAY DIFFRACTION96.13
3.12-3.570.17511380.15854449X-RAY DIFFRACTION96.08
3.57-4.490.14731390.12764509X-RAY DIFFRACTION96.27
4.49-53.250.14871440.15464625X-RAY DIFFRACTION94.89
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)
13.46231627386-0.02777538739270.07837715342372.116985535470.546721330791.788768763-0.069523112985-0.1639020543240.410013565460.03055412730340.0725266706288-0.17198876174-0.2498962806630.20538299333-0.08332096514770.305735338961-0.0589675722461-0.0241106179530.246902598260.0506916844840.3490616843629.429458842119.623200157543.8282725913
21.98379661783-0.215823777415-0.02161326526492.27020540307-0.3467496394591.19641948202-0.02777695888310.162641132439-0.273556240658-0.0598266272125-0.02102422896270.07872425237820.08729310077640.04140891445430.04807053188710.224292986155-0.0217070900574-0.02662348975620.227657674673-0.001974737437650.33856858781821.17074201039.6455919832136.2881759207
34.428251241520.1373235439741.248715629981.078643276850.3482701638090.7126326526540.08316881906080.1997651811560.205767583212-0.00739673997870.0161339925097-0.0802570559904-0.06661047092430.044910518431-0.04856432961030.297981579299-0.0546193889892-0.02227870712610.2693248273730.06101748215870.33304009740634.360644650927.208051718535.7981957902
45.880601301922.839755614450.7755798336427.769995043340.3171333661673.60510032915-0.04836750529310.0561673317938-0.192396871827-0.0457553440162-0.05647195192010.318152951618-0.267335632224-0.06643032285210.08740052806320.1878339811490.0324132698429-0.009380054607790.2028773336940.05133100608050.26165232428914.46555452724.816506906736.9462763115
51.42804978693-0.2210396439440.03365528613783.206150784990.1415481077111.052180629810.084592272470.04940155324830.0260201631230.0157358450535-0.07746303951660.0225712328878-0.0156250307612-0.0621900973779-0.02023154772740.197213971168-0.0183744088224-0.004931163526480.226509062680.01892454292750.17083477360665.544556041951.255204652847.4698294883
61.236143380610.9529205797620.5612515214514.052301744971.091429613590.9835546592220.0967964214214-0.0220460951817-0.08298672228750.278362024815-0.09866248891120.3316686062360.0582880756766-0.197324385837-0.003824013040130.26022074963-0.0338713035050.05310916940850.327273853188-0.008751054033110.32140394753752.149021362844.953809281651.6147423639
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 48 )AA1 - 481 - 48
22chain 'A' and (resid 49 through 154 )AA49 - 15449 - 154
33chain 'A' and (resid 155 through 244 )AA155 - 244155 - 244
44chain 'A' and (resid 245 through 269 )AA245 - 269245 - 269
55chain 'B' and (resid 3 through 154 )BG3 - 1541 - 152
66chain 'B' and (resid 155 through 268 )BG155 - 268153 - 266

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