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- PDB-8bic: O-Methyltransferase Plu4891 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 8bic
TitleO-Methyltransferase Plu4891 in complex with SAH
Componentsmethyltransferase Plu4891
KeywordsTRANSFERASE / methyltransferase / polyketide / anthraquinone
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / 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-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionNov 2, 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
Revision 1.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: methyltransferase Plu4891
B: methyltransferase Plu4891
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7877
Polymers76,8802
Non-polymers9075
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-67 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.280, 57.940, 97.180
Angle α, β, γ (deg.)90.000, 121.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-530-

HOH

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Components

#1: Protein methyltransferase Plu4891


Mass: 38439.875 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: A0A6L9JRI9
#2: 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M D/L malic acid

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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: Sep 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 67228 / % possible obs: 96 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.3
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2 / Num. unique obs: 9857 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BGT

8bgt


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 12.584 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 3361 5 %RANDOM
Rwork0.1883 ---
obs0.1902 63854 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.64 Å2 / Biso mean: 29.407 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1-4.67 Å20 Å2-3.93 Å2
2--6.25 Å2-0 Å2
3----3.42 Å2
Refinement stepCycle: final / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 60 253 5450
Biso mean--26.28 41.03 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135345
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174963
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.6247219
X-RAY DIFFRACTIONr_angle_other_deg1.1841.57811554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75223.955268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95315984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9511520
X-RAY DIFFRACTIONr_chiral_restr0.0520.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021077
X-RAY DIFFRACTIONr_rigid_bond_restr4.478310306
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 248 -
Rwork0.431 4715 -
all-4963 -
obs--97.54 %
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)
10.031-0.02020.00920.0455-0.01890.37720.00310.015-0.0019-0.0128-0.00140.0072-0.0202-0.0205-0.00170.0198-0.00030.01030.0106-0.00020.065-1.055728.682128.7417
20.05430.0161-0.08840.0527-0.02880.2421-0.0008-0.0012-0.00750.0119-0.0039-0.0005-0.0009-0.00010.00470.02330.00030.0120.00040.00050.06542.267222.511564.2328
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 401
2X-RAY DIFFRACTION2B-5 - 401

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