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- PDB-8bgt: O-Methyltransferase Plu4890 in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 8bgt
TitleO-Methyltransferase Plu4890 in complex with SAM
ComponentsMethyltransferase Plu4890
KeywordsTRANSFERASE / methyltransferase / polyketide / anthraquinone
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / TRYPTOPHAN / Methyltransferase
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsHuber, E.M. / Groll, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments.
Authors: Huber, E.M. / Kreling, L. / Heinrich, A.K. / Dunnebacke, M. / Pothig, A. / Bode, H.B. / Groll, M.
History
DepositionOct 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 17, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase Plu4890
B: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,56310
Polymers73,1012
Non-polymers1,4628
Water1,22568
1
A: Methyltransferase Plu4890
hetero molecules

A: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,04314
Polymers73,1012
Non-polymers1,94212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7520 Å2
ΔGint-31 kcal/mol
Surface area26410 Å2
MethodPISA
2
B: Methyltransferase Plu4890
hetero molecules

B: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0826
Polymers73,1012
Non-polymers9814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area6700 Å2
ΔGint-35 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.260, 76.780, 169.150
Angle α, β, γ (deg.)90.000, 96.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-518-

HOH

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Components

#1: Protein Methyltransferase Plu4890


Mass: 36550.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6L9JR93
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NaF, 0.1 M bis-tris propane pH 7.5, 20% PEG3350

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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: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→48 Å / Num. obs: 42753 / % possible obs: 97.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 10.9
Reflection shellResolution: 2.15→2.25 Å / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5475 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 30.255 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 2137 5 %RANDOM
Rwork0.223 ---
obs0.2252 40598 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.76 Å2 / Biso mean: 73.39 Å2 / Biso min: 42.92 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å2-0 Å20.83 Å2
2---3.8 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 99 68 5315
Biso mean--75.84 74.33 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135367
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174923
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.6287228
X-RAY DIFFRACTIONr_angle_other_deg1.0841.57811421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0722.799293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65215948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4911529
X-RAY DIFFRACTIONr_chiral_restr0.040.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021181
X-RAY DIFFRACTIONr_rigid_bond_restr0.51310289
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 155 -
Rwork0.413 2952 -
all-3107 -
obs--97.25 %
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)
10.8848-0.00940.55670.2834-0.03590.60480.32320.2351-0.1654-0.0066-0.18240.01460.13770.042-0.14070.3790.1551-0.23220.2992-0.06470.171-13.898110.802265.48
21.03470.1318-0.5560.1783-0.49652.3725-0.2197-0.34680.2871-0.17950.05870.040.21730.19420.1610.7060.1474-0.30810.2677-0.10090.2166-26.063531.86418.1229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 402
2X-RAY DIFFRACTION2B0 - 401

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