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- PDB-8bgy: O-Methyltransferase Plu4890 in complex with SAH and AQ-284a -

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Basic information

Entry
Database: PDB / ID: 8bgy
TitleO-Methyltransferase Plu4890 in complex with SAH and AQ-284a
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
1,3-dimethoxy-8-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: 1.95 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)148,93514
Polymers146,2024
Non-polymers2,73310
Water7,909439
1
A: Methyltransferase Plu4890
B: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4747
Polymers73,1012
Non-polymers1,3735
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-32 kcal/mol
Surface area25890 Å2
MethodPISA
2
D: Methyltransferase Plu4890
hetero molecules

C: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4617
Polymers73,1012
Non-polymers1,3605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area6100 Å2
ΔGint-39 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.130, 77.260, 166.880
Angle α, β, γ (deg.)90.000, 95.490, 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 , 5 types, 449 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-QP3 / 1,3-dimethoxy-8-oxidanyl-anthracene-9,10-dione


Mass: 284.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium acetate, 0.1 M Sodium cacodylate pH 6.5, 30 % PEG8000

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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: May 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48 Å / Num. obs: 116636 / % possible obs: 97 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.2
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2 / Num. unique obs: 15941 / % possible all: 98.5

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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: 1.95→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.023 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.461 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 5655 5 %RANDOM
Rwork0.2 ---
obs0.201 107439 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.28 Å2 / Biso mean: 38.747 Å2 / Biso min: 22.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20.55 Å2
2---0.73 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10296 0 190 440 10926
Biso mean--40.28 42.92 -
Num. residues----1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310815
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610076
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.6414600
X-RAY DIFFRACTIONr_angle_other_deg1.0581.58923203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68751292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98622.842584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.472151912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2861557
X-RAY DIFFRACTIONr_chiral_restr0.0350.21342
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212271
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022607
X-RAY DIFFRACTIONr_rigid_bond_restr0.167320891
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 424 -
Rwork0.291 8047 -
all-8471 -
obs--98.58 %
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)
10.1341-0.0232-0.08850.0687-0.05380.3966-0.0143-0.03380.00520.00620.0097-0.0012-0.01960.03170.00470.02430.0068-0.02640.059-0.00510.031223.0728-11.30817.2588
20.08050.0229-0.01690.03750.08530.3951-0.01080.01710.0014-0.01110.00480.0056-0.0239-0.01620.00610.0262-0.0046-0.02840.04890.00380.033510.4516-12.2831-18.2837
30.27280.09890.10640.08980.02960.15020.0259-0.0367-0.0140.0143-0.0172-0.00670.0045-0.0115-0.00870.0201-0.0021-0.02510.05650.00130.034427.1236.2353-64.198
40.19670.04280.11520.07370.02740.22110.015-0.0215-0.01280.0107-0.0075-0.0060.00870.0012-0.00750.0172-0.0007-0.02420.05450.0010.0355-3.0117-33.3021-65.0002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 402
2X-RAY DIFFRACTION2B0 - 402
3X-RAY DIFFRACTION3C0 - 402
4X-RAY DIFFRACTION4D0 - 402

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