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- PDB-7owb: Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region ... -

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Basic information

Entry
Database: PDB / ID: 7owb
TitleChimeric carminomycin-4-O-methyltransferase (DnrK) with a region from 10-hydroxylase CalMB
ComponentsCarminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / aclacinomycin 10-hydroxylase
Function / homology
Function and homology information


carminomycin 4-O-methyltransferase / daunorubicin biosynthetic process / O-methyltransferase activity / methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / 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
Chem-3VL / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein / Carminomycin 4-O-methyltransferase DnrK
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
Streptomyces sp. ZEA17I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDinis, P. / MetsaKetela, M.
CitationJournal: Pnas Nexus / Year: 2023
Title: Evolution-inspired engineering of anthracycline methyltransferases.
Authors: Dinis, P. / Tirkkonen, H. / Wandi, B.N. / Siitonen, V. / Niemi, J. / Grocholski, T. / Metsa-Ketela, M.
History
DepositionJun 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2593
Polymers40,3051
Non-polymers9542
Water57632
1
A: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein
hetero molecules

A: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5176
Polymers80,6092
Non-polymers1,9084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5890 Å2
ΔGint-48 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.800, 103.137, 66.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein / COMT / Anthracycline 4-O-methyltransferase


Mass: 40304.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius (bacteria), (gene. exp.) Streptomyces sp. ZEA17I (bacteria)
Gene: dnrK, DKT74_09280 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q06528, UniProt: A0A2V2Q0Q4, carminomycin 4-O-methyltransferase
#2: Chemical ChemComp-3VL / methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate / aclacinomycin T


Mass: 569.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H35NO10 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryocooling / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.45→44.87 Å / Num. obs: 15812 / % possible obs: 99.13 % / Redundancy: 5.69 % / Biso Wilson estimate: 51.87 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.19
Reflection shellResolution: 2.45→2.59 Å / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 5507

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TW2

1tw2


Resolution: 2.45→44.87 Å / SU ML: 0.4449 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1495
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2647 771 4.88 %
Rwork0.2467 15037 -
obs0.2475 15808 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.76 Å2
Refinement stepCycle: LAST / Resolution: 2.45→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 67 32 2594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112616
X-RAY DIFFRACTIONf_angle_d1.41383580
X-RAY DIFFRACTIONf_chiral_restr0.0787429
X-RAY DIFFRACTIONf_plane_restr0.0335453
X-RAY DIFFRACTIONf_dihedral_angle_d17.1656929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.60.43961350.45212370X-RAY DIFFRACTION97.02
2.6-2.80.42691260.37692494X-RAY DIFFRACTION99.58
2.8-3.090.3661320.33192470X-RAY DIFFRACTION99.54
3.09-3.530.27431220.25782518X-RAY DIFFRACTION99.89
3.53-4.450.19541270.21232532X-RAY DIFFRACTION99.48
4.45-44.870.21751290.18672653X-RAY DIFFRACTION99.25

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