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- PDB-8bih: O-Methyltransferase Plu4890 in complex with SAH and AQ-284b -

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Basic information

Entry
Database: PDB / ID: 8bih
TitleO-Methyltransferase Plu4890 in complex with SAH and AQ-284b
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
3,8-dimethoxy-1-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: 2.4 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

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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
I: Methyltransferase Plu4890
J: Methyltransferase Plu4890
K: Methyltransferase Plu4890
L: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,15041
Polymers438,60612
Non-polymers7,54329
Water3,297183
1
A: Methyltransferase Plu4890
L: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1906
Polymers73,1012
Non-polymers1,0894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-37 kcal/mol
Surface area25650 Å2
MethodPISA
2
B: Methyltransferase Plu4890
E: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4386
Polymers73,1012
Non-polymers1,3374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-33 kcal/mol
Surface area25610 Å2
MethodPISA
3
C: Methyltransferase Plu4890
G: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63710
Polymers73,1012
Non-polymers1,5368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-59 kcal/mol
Surface area25430 Å2
MethodPISA
4
D: Methyltransferase Plu4890
K: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2697
Polymers73,1012
Non-polymers1,1685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-43 kcal/mol
Surface area25660 Å2
MethodPISA
5
F: Methyltransferase Plu4890
H: 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
Buried area6200 Å2
ΔGint-41 kcal/mol
Surface area25290 Å2
MethodPISA
6
I: Methyltransferase Plu4890
J: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1545
Polymers73,1012
Non-polymers1,0533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-32 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.000, 91.130, 150.410
Angle α, β, γ (deg.)89.960, 106.180, 119.970
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Methyltransferase Plu4890


Mass: 36550.527 Da / Num. of mol.: 12
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, 212 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-QOT / 3,8-dimethoxy-1-oxidanyl-anthracene-9,10-dione


Mass: 284.263 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.5 M Lithium chloride, 0.1 M Tris pH 8.5, 28% PEG6000

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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: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48 Å / Num. obs: 143304 / % possible obs: 92.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 6.2
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 16771 / % possible all: 94.2

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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: 2.4→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.889 / SU B: 40.997 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.21 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 7163 5 %RANDOM
Rwork0.2674 ---
obs0.2688 136095 92.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.88 Å2 / Biso mean: 54.099 Å2 / Biso min: 21.03 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å2-1.05 Å22.09 Å2
2---2.98 Å21.47 Å2
3---4.15 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30888 0 519 183 31590
Biso mean--63.88 41.37 -
Num. residues----3828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01332101
X-RAY DIFFRACTIONr_bond_other_d0.0010.01529944
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.63743293
X-RAY DIFFRACTIONr_angle_other_deg1.0451.58768931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8653818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42722.8821742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.718155667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.14715169
X-RAY DIFFRACTIONr_chiral_restr0.0340.23997
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0236298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027708
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 542 -
Rwork0.401 10291 -
all-10833 -
obs--94.36 %
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)
10.3834-0.06150.11960.3179-0.32540.3707-0.05340.0202-0.006900.03460.0123-0.0261-0.02850.01880.0894-0.0069-0.01390.088-0.12640.204863.91559.302444.4901
20.5511-0.06330.05870.2130.22220.2910.0094-0.05330.1009-0.02210.0342-0.04450.02410.0311-0.04360.07410.0019-0.01880.1014-0.1460.215234.66877.8621-4.5138
30.4196-0.16840.18730.5273-0.34110.94290.0111-0.0026-0.0278-0.0502-0.04610.1066-0.064-0.00350.0350.04040.0255-0.04780.1081-0.15020.217962.43696.1571-26.9912
40.4273-0.1691-0.24590.23130.16280.3437-0.02220.03860.02590.0434-0.07160.02230.039-0.05370.09370.0677-0.0133-0.00820.1008-0.12470.224932.6457-44.2483-4.7533
50.2889-0.015-0.10420.10480.2410.6421-0.01180.0568-0.09540.0363-0.0219-0.00450.0089-0.07080.03380.0935-0.0045-0.01360.1498-0.1630.189920.3127-18.4949-27.4004
60.1721-0.0920.17290.48350.03060.2459-0.06170.02260.0260.12980.0046-0.1058-0.0238-0.02250.05710.15530.0052-0.07130.0925-0.11270.173835.94857.12466.9563
70.2979-0.21190.12190.4133-0.39890.61770.01640.0427-0.15290.0218-0.06620.0157-0.07690.01450.04980.0459-0.0099-0.01920.125-0.14430.26278.8091-19.8314-5.08
80.6869-0.3590.08220.32840.16020.37640.04130.1127-0.1895-0.0026-0.06450.1196-0.05270.01980.02320.0979-0.0079-0.03340.1155-0.15440.228819.8808-18.461844.399
90.3264-0.1331-0.34070.3693-0.10940.5842-0.0398-0.02290.0641-0.0176-0.0255-0.09150.0572-0.00780.06530.08030.0069-0.03430.1139-0.14040.229565.9939-42.99144.703
100.5840.1069-0.16240.0765-0.00280.4723-0.0174-0.03960.11140.017-0.00160.03280.0343-0.01350.0190.08640.0169-0.01320.1201-0.16140.227435.504-41.802166.8783
110.41-0.2042-0.26960.2455-0.02690.54850.04680.01640.1289-0.0514-0.0773-0.06540.0424-0.01520.03050.04720.0113-0.00370.0703-0.08540.247562.978-43.2919-27.2856
120.8546-0.1799-0.01790.2635-0.20660.651-0.1125-0.1227-0.3728-0.01550.0320.1316-0.07720.03310.08050.0560.00920.01850.04760.00250.316678.1423-17.439867.131
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
9X-RAY DIFFRACTION9I0 - 402
10X-RAY DIFFRACTION10J0 - 900
11X-RAY DIFFRACTION11K0 - 401
12X-RAY DIFFRACTION12L0 - 900

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