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- PDB-8bib: O-Methyltransferase Plu4890 in complex with SAH and AQ-256 -

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Basic information

Entry
Database: PDB / ID: 8bib
TitleO-Methyltransferase Plu4890 in complex with SAH and AQ-256
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
CARBONATE ION / 1,3,8-tris(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: 2.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,22621
Polymers146,2024
Non-polymers3,02417
Water8,827490
1
A: Methyltransferase Plu4890
B: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,61710
Polymers73,1012
Non-polymers1,5168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-41 kcal/mol
Surface area25620 Å2
MethodPISA
2
D: Methyltransferase Plu4890
hetero molecules

C: Methyltransferase Plu4890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,60911
Polymers73,1012
Non-polymers1,5089
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_344-x-2,y-1/2,-z-11
Buried area6920 Å2
ΔGint-59 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.060, 77.050, 167.220
Angle α, β, γ (deg.)90.000, 95.500, 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 , 7 types, 507 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-QOI / 1,3,8-tris(oxidanyl)anthracene-9,10-dione


Mass: 256.210 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 55.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M NaI, 0.1 M bis-tris propane pH 6.5, 20% PEG3350

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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: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48 Å / Num. obs: 68830 / % possible obs: 96.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.1
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2 / Num. unique obs: 8321

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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: 2.3→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.196 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 3440 5 %RANDOM
Rwork0.2136 ---
obs0.2155 65359 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 276 Å2 / Biso mean: 45.363 Å2 / Biso min: 26.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å21.08 Å2
2--1 Å2-0 Å2
3----3.32 Å2
Refinement stepCycle: final / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10296 0 206 492 10994
Biso mean--42.31 51.3 -
Num. residues----1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310725
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179750
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.63914465
X-RAY DIFFRACTIONr_angle_other_deg1.0841.58122622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77851272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62522.897580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.831151888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6711556
X-RAY DIFFRACTIONr_chiral_restr0.0380.21332
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022356
X-RAY DIFFRACTIONr_rigid_bond_restr0.233320475
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 255 -
Rwork0.277 4849 -
all-5104 -
obs--98.25 %
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)
10.0975-0.0195-0.07080.0369-0.06620.2775-0.0099-0.01820.00610.00440.00850.0037-0.01060.0160.00140.01350.0015-0.02690.0154-0.00430.0612-40.0295-11.045317.222
20.0832-0.0287-0.04320.03310.04540.2581-0.01330.00720.0001-0.00410.01070.0041-0.0083-0.01110.00260.0147-0.0057-0.02570.01180.00280.0627-52.7484-11.889-18.2531
30.12770.04960.0650.02120.02940.12440.0133-0.0157-0.00830.0045-0.0113-0.0023-0.0022-0.007-0.0020.0105-0.0027-0.02420.01790.00340.0648-35.98026.4299-64.34
40.0985-0.01920.08260.0150.0090.1330.0076-0.0032-0.0084-0.0001-0.0023-0.00050.00620.0031-0.00540.0087-0.0029-0.02260.02110.00320.0616-66.088-32.912-65.2119
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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