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- PDB-8bgx: O-Methyltransferase Plu4890 in complex with SAH and AQ-270a -

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Basic information

Entry
Database: PDB / ID: 8bgx
TitleO-Methyltransferase Plu4890 in complex with SAH and AQ-270a
ComponentsMethyltransferase Plu4890
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
1-methoxy-3,8-bis(oxidanyl)anthracene-9,10-dione / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
Revision 1.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: Methyltransferase Plu4890
D: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,35424
Polymers146,2024
Non-polymers3,15220
Water8,629479
1
A: Methyltransferase Plu4890
D: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,66513
Polymers73,1012
Non-polymers1,56411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-93 kcal/mol
Surface area25650 Å2
MethodPISA
2
B: Methyltransferase Plu4890
hetero molecules

C: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,68811
Polymers73,1012
Non-polymers1,5879
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area7010 Å2
ΔGint-67 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.140, 78.370, 167.730
Angle α, β, γ (deg.)90.000, 96.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Methyltransferase Plu4890


Mass: 36550.527 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 499 molecules

#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-QPF / 1-methoxy-3,8-bis(oxidanyl)anthracene-9,10-dione


Mass: 270.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 25% PEG10000

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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: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47 Å / Num. obs: 124883 / % possible obs: 97.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 17928 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BGT

8bgt


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 10.756 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 6243 5 %RANDOM
Rwork0.179 ---
obs0.1811 118613 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.6 Å2 / Biso mean: 40.395 Å2 / Biso min: 20.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å2-0 Å22.37 Å2
2---3.26 Å2-0 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10296 0 211 480 10987
Biso mean--50.8 44.5 -
Num. residues----1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310848
X-RAY DIFFRACTIONr_bond_other_d0.0010.01510075
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.63914650
X-RAY DIFFRACTIONr_angle_other_deg1.1451.58723209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06351299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5122.84588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.378151908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8951558
X-RAY DIFFRACTIONr_chiral_restr0.0450.21346
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212333
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022615
X-RAY DIFFRACTIONr_rigid_bond_restr1.172320923
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 463 -
Rwork0.257 8797 -
all-9260 -
obs--98.89 %

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