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- PDB-8bie: O-Methyltransferase Plu4894 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 8bie
TitleO-Methyltransferase Plu4894 in complex with SAH
Componentsmethyltransferase Plu4894
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
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
B: methyltransferase Plu4894
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8374
Polymers72,0682
Non-polymers7692
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-33 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.910, 79.950, 96.510
Angle α, β, γ (deg.)90.000, 99.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein methyltransferase Plu4894


Mass: 36034.211 Da / Num. of mol.: 2
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium chloride, 0.1 M Hepes pH 7.0, 20% 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: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→47 Å / Num. obs: 31411 / % possible obs: 98.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.8
Reflection shellResolution: 2.25→2.35 Å / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3841 / % possible all: 98.9

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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: 2.25→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 18.962 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1570 5 %RANDOM
Rwork0.1974 ---
obs0.199 29827 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.25 Å2 / Biso mean: 50.416 Å2 / Biso min: 30.95 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å20 Å20.77 Å2
2---2.39 Å20 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5060 0 52 66 5178
Biso mean--53 48.43 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135210
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174878
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.6247032
X-RAY DIFFRACTIONr_angle_other_deg1.0641.58211348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85723.672256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69715960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1261522
X-RAY DIFFRACTIONr_chiral_restr0.0410.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021042
X-RAY DIFFRACTIONr_rigid_bond_restr0.214310088
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 114 -
Rwork0.353 2168 -
all-2282 -
obs--98.45 %
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)
10.170.1017-0.22690.2769-0.18350.62530.0293-0.03080.01650.0281-0.01060.0172-0.0398-0.014-0.01870.01070.00380.00920.045-0.00530.0176-19.9175-19.6726-9.1997
20.17220.1545-0.2290.1684-0.1970.557-0.0211-0.0253-0.0176-0.0393-0.0071-0.03620.03530.03660.02810.02580.01010.02050.03820.00020.0182-1.2792-22.8585-41.0198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 900
2X-RAY DIFFRACTION2B0 - 900

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