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- PDB-8bgz: O-Methyltransferase Plu4890 (mutant H229N) in complex with SAH an... -

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Basic information

Entry
Database: PDB / ID: 8bgz
TitleO-Methyltransferase Plu4890 (mutant H229N) in complex with SAH and AQ-256
Componentsmethyltransferase Plu4890 H229N mutant
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
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 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 H229N mutant
B: methyltransferase Plu4890 H229N mutant
C: methyltransferase Plu4890 H229N mutant
D: methyltransferase Plu4890 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,33620
Polymers146,1064
Non-polymers3,23016
Water10,088560
1
A: methyltransferase Plu4890 H229N mutant
B: methyltransferase Plu4890 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,72611
Polymers73,0532
Non-polymers1,6739
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-42 kcal/mol
Surface area25870 Å2
MethodPISA
2
C: methyltransferase Plu4890 H229N mutant
hetero molecules

D: methyltransferase Plu4890 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6109
Polymers73,0532
Non-polymers1,5587
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_354-x-2,y+1/2,-z-11
Buried area6650 Å2
ΔGint-33 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.350, 77.590, 167.600
Angle α, β, γ (deg.)90.000, 95.270, 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 H229N mutant


Mass: 36526.480 Da / Num. of mol.: 4 / Mutation: H229N
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, 576 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium nitrate, 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: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48 Å / Num. obs: 107159 / % possible obs: 97.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 14700 / % possible all: 99

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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→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.544 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.908 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 5356 5 %RANDOM
Rwork0.1715 ---
obs0.1734 101773 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.32 Å2 / Biso mean: 37.052 Å2 / Biso min: 18.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20.78 Å2
2--1.34 Å2-0 Å2
3----2.25 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10288 0 223 563 11074
Biso mean--36.2 44.77 -
Num. residues----1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310786
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179821
X-RAY DIFFRACTIONr_angle_refined_deg1.141.63914549
X-RAY DIFFRACTIONr_angle_other_deg1.1171.58122798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91851284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47322.973582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34151899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6281556
X-RAY DIFFRACTIONr_chiral_restr0.0420.21338
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022365
X-RAY DIFFRACTIONr_rigid_bond_restr0.414320607
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 399 -
Rwork0.227 7590 -
all-7989 -
obs--99.11 %
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)
10.0447-0.0133-0.03640.027-0.02760.0944-0.0036-0.01180.00270.0040.0027-0.0009-0.00410.01050.00090.0110.002-0.01770.0033-0.00280.0295-40.0189-11.328517.2451
20.01810.01080.01190.01420.03440.105-0.00650.0053-0.0008-0.00760.00240.0026-0.01460.00180.0040.0131-0.0027-0.01760.00170.00160.0306-53.1269-12.3634-18.1012
30.07810.02930.0320.01830.01440.04090.0101-0.0105-0.00480.0046-0.0071-0.00170.0046-0.0025-0.00310.0091-0.0017-0.01610.0030.00050.0317-36.66956.7256-64.6211
40.04340.00570.0220.01760.00940.06250.005-0.0058-0.00340.0034-0.0017-0.00110.00430.0053-0.00330.0082-0.0007-0.01560.00230.00030.0318-66.7554-32.9954-65.3667
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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