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- PDB-8bij: O-Methyltransferase Plu4894 (mutant I88M, W91L, C97Y, S142L, G146... -

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Basic information

Entry
Database: PDB / ID: 8bij
TitleO-Methyltransferase Plu4894 (mutant I88M, W91L, C97Y, S142L, G146V, Y258M, L270F, S309Y) in complex with SAH
ComponentsMethyltransferase Plu4894 mutant I88M, W91L, C97Y, S142L, G146V, Y258M, L270F, S309Y
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
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 Plu4894 mutant I88M, W91L, C97Y, S142L, G146V, Y258M, L270F, S309Y
B: Methyltransferase Plu4894 mutant I88M, W91L, C97Y, S142L, G146V, Y258M, L270F, S309Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,44311
Polymers72,3712
Non-polymers1,0729
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-66 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.310, 76.460, 113.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methyltransferase Plu4894 mutant I88M, W91L, C97Y, S142L, G146V, Y258M, L270F, S309Y


Mass: 36185.520 Da / Num. of mol.: 2
Mutation: I88M, W91L, C97Y, S142L, G146V, Y258M, L270F, S309Y
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: A0A6L9JNN3

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Non-polymers , 5 types, 254 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Sodium acetate pH 4.6, 8% 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: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→47 Å / Num. obs: 91131 / % possible obs: 99.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 24.6
Reflection shellResolution: 1.55→1.65 Å / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 12119

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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: 8BIE

8bie


Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.705 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 4556 5 %RANDOM
Rwork0.189 ---
obs0.1905 86562 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.91 Å2 / Biso mean: 29.465 Å2 / Biso min: 18.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å2-0 Å2-0 Å2
2---3.86 Å20 Å2
3---5.74 Å2
Refinement stepCycle: final / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 68 247 5395
Biso mean--29.06 38.36 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135371
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175048
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.6267266
X-RAY DIFFRACTIONr_angle_other_deg1.221.58211760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95423.74262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.921151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7231522
X-RAY DIFFRACTIONr_chiral_restr0.0540.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021077
X-RAY DIFFRACTIONr_rigid_bond_restr4.675310419
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 336 -
Rwork0.286 6379 -
all-6715 -
obs--99.54 %

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