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- PDB-8bh0: O-Methyltransferase Plu4890 in complex with SAH and AQ-270b -

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Basic information

Entry
Database: PDB / ID: 8bh0
TitleO-Methyltransferase Plu4890 in complex with SAH and AQ-270b
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
3-methoxy-1,8-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: 1.7 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
E: Methyltransferase Plu4890
F: Methyltransferase Plu4890
G: Methyltransferase Plu4890
H: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,88633
Polymers292,4048
Non-polymers5,48125
Water15,385854
1
A: Methyltransferase Plu4890
D: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5049
Polymers73,1012
Non-polymers1,4037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-56 kcal/mol
Surface area26020 Å2
MethodPISA
2
B: Methyltransferase Plu4890
E: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4568
Polymers73,1012
Non-polymers1,3556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-46 kcal/mol
Surface area26290 Å2
MethodPISA
3
C: Methyltransferase Plu4890
F: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4929
Polymers73,1012
Non-polymers1,3917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-57 kcal/mol
Surface area25850 Å2
MethodPISA
4
G: Methyltransferase Plu4890
hetero molecules

H: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4337
Polymers73,1012
Non-polymers1,3325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_544x,y-1,z-11
Buried area6130 Å2
ΔGint-33 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.940, 105.620, 124.470
Angle α, β, γ (deg.)94.370, 90.220, 104.970
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Methyltransferase Plu4890


Mass: 36550.527 Da / Num. of mol.: 8
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, 879 molecules

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


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


Mass: 270.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 854 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammoniumsulfate, 0.1 M MES pH 6.5, 30 % PEG5000MME

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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: 1.7→49 Å / Num. obs: 291332 / % possible obs: 94.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.5
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2 / Num. unique obs: 45939 / % possible all: 94.7

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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: 1.7→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.55 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 14564 5 %RANDOM
Rwork0.1776 ---
obs0.179 276726 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.53 Å2 / Biso mean: 30.708 Å2 / Biso min: 19.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20.17 Å20.29 Å2
2---0.03 Å20.75 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20592 0 377 855 21824
Biso mean--35.1 38.01 -
Num. residues----2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01321620
X-RAY DIFFRACTIONr_bond_other_d0.0010.01520085
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.63929205
X-RAY DIFFRACTIONr_angle_other_deg1.1351.58746262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29952590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98122.9071173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.326153808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.33715114
X-RAY DIFFRACTIONr_chiral_restr0.0440.22687
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0224602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025210
X-RAY DIFFRACTIONr_rigid_bond_restr0.336341705
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 1084 -
Rwork0.275 20604 -
all-21688 -
obs--95.26 %
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)
10.1672-0.0445-0.08560.1482-0.0090.09330.0076-0.01370.03250.025-0.00030.00010.01030.0179-0.00730.06320.00620.0070.0383-0.01030.0345-28.3401-17.106320.3339
20.2751-0.04060.08920.11010.03510.0717-0.0352-0.03750.01560.01750.0439-0.00670.0035-0.007-0.00870.06280.0048-0.01450.0622-0.01410.0168-16.408512.6828-15.012
30.0838-0.05570.06410.0550.01840.4731-0.01070.0001-0.01380.00610.01960.0061-0.03730.0207-0.0090.0603-0.00530.00190.0336-0.00190.0335-10.7134-41.078451.3722
40.28050.0587-0.07810.08220.03550.0784-0.03160.0461-0.0234-0.01650.0393-0.0051-0.0098-0.0048-0.00770.06840.00420.01720.0573-0.00850.0227-16.8804-28.0867-14.0644
50.1530.02750.07250.16350.00170.11340.01810.0048-0.0276-0.0304-0.00330.0172-0.01030.023-0.01480.0628-0.0023-0.00720.0423-0.01250.0301-27.90971.6058-49.3914
60.26580.09790.07320.05180.09930.46190.01260.0036-0.0045-0.0103-0.00130.00670.0013-0.023-0.01130.0695-0.0059-0.01680.0059-0.00950.0526-29.6737-53.934821.045
70.3209-0.0989-0.08590.04350.07120.43580.0174-0.00680.04270.01280.00120.00520.0002-0.0183-0.01870.06080.00520.02340.0046-0.01070.0658-1.2876-63.5605-50.1773
80.06620.012-0.06470.0542-0.00810.468-0.00230.00260.0239-0.00660.00750.01520.04280.0236-0.00520.0589-0.0037-0.00340.03510.00010.0346-10.182815.599643.6032
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
5X-RAY DIFFRACTION5E0 - 402
6X-RAY DIFFRACTION6F0 - 402
7X-RAY DIFFRACTION7G0 - 402
8X-RAY DIFFRACTION8H0 - 402

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