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

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Basic information

Entry
Database: PDB / ID: 8bid
TitleO-Methyltransferase Plu4890 (mutant H229N) in complex with SAH and AQ-270a
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-methoxy-3,8-bis(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: 1.75 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 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)149,85641
Polymers146,1064
Non-polymers3,75037
Water9,872548
1
C: methyltransferase Plu4890 H229N mutant
hetero molecules

A: methyltransferase Plu4890 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63812
Polymers73,0532
Non-polymers1,58510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y+1/2,-z+21
Buried area7070 Å2
ΔGint-73 kcal/mol
Surface area25940 Å2
MethodPISA
2
B: methyltransferase Plu4890 H229N mutant
D: methyltransferase Plu4890 H229N mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,21729
Polymers73,0532
Non-polymers2,16427
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-169 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.400, 77.670, 167.330
Angle α, β, γ (deg.)90.000, 95.490, 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 , 6 types, 585 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-QPF / 1-methoxy-3,8-bis(oxidanyl)anthracene-9,10-dione


Mass: 270.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 56.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25 % PEG4000

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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: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→49 Å / Num. obs: 159145 / % possible obs: 97.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.1
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2 / Num. unique obs: 24786 / % possible all: 99.5

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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: 1.75→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 8.915 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 7956 5 %RANDOM
Rwork0.18 ---
obs0.1819 151158 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 641.01 Å2 / Biso mean: 33.681 Å2 / Biso min: 17.16 Å2
Baniso -1Baniso -2Baniso -3
1-5.25 Å2-0 Å2-1.29 Å2
2---3.01 Å20 Å2
3----1.95 Å2
Refinement stepCycle: final / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10282 0 243 551 11076
Biso mean--38.23 43.95 -
Num. residues----1275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01310880
X-RAY DIFFRACTIONr_bond_other_d0.0030.01510119
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.63914690
X-RAY DIFFRACTIONr_angle_other_deg1.2531.58723309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50251304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75522.93587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.207151912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4321557
X-RAY DIFFRACTIONr_chiral_restr0.0640.21348
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212373
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022625
X-RAY DIFFRACTIONr_rigid_bond_restr9.518320999
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 596 -
Rwork0.351 11316 -
all-11912 -
obs--99.64 %

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