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

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Basic information

Entry
Database: PDB / ID: 7phd
TitleChimeric carminomycin-4-O-methyltransferase (DnrK) with a region from 10-decarboxylase TamK
ComponentsCarminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / tsukubarubicin 10-decarboxylase
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-ADENOSYLMETHIONINE / Methyltransferase domain-containing protein / Carminomycin 4-O-methyltransferase DnrK
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
Streptomyces tsukubensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsGrocholski, T. / Dinis, P. / MetsaKetela, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionAug 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 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
B: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,88613
Polymers80,2892
Non-polymers2,59711
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-87 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.509, 101.321, 62.968
Angle α, β, γ (deg.)90.000, 102.292, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40144.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius (bacteria), (gene. exp.) Streptomyces tsukubensis (strain DSM 42081 / NBRC 108919 / NRRL 18488 / 9993) (bacteria)
Gene: dnrK, STSU_011780, STSU_11775 / Strain: DSM 42081 / NBRC 108919 / NRRL 18488 / 9993 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q06528, UniProt: I2N5E8, carminomycin 4-O-methyltransferase

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Non-polymers , 5 types, 345 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: 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.: 2 / Source method: obtained synthetically / Formula: C30H35NO10 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Magnesium chloride hexahydrate; 0.1 M Tris-HCl, pH=8.0; 20 % w/v PEG 6000

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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 PILATUS 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: 1.53→100 Å / Num. obs: 300031 / % possible obs: 98.1 % / Redundancy: 2.69 % / Biso Wilson estimate: 18.15 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.18
Reflection shellResolution: 1.53→1.57 Å / Rmerge(I) obs: 0.588 / Num. unique obs: 21078

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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: 1.53→48.04 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.2026
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 1996 1.82 %
Rwork0.2205 107428 -
obs0.2209 109424 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.24 Å2
Refinement stepCycle: LAST / Resolution: 1.53→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4769 0 174 334 5277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01095043
X-RAY DIFFRACTIONf_angle_d1.36956900
X-RAY DIFFRACTIONf_chiral_restr0.0733827
X-RAY DIFFRACTIONf_plane_restr0.0339859
X-RAY DIFFRACTIONf_dihedral_angle_d13.24681768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.3351300.33257630X-RAY DIFFRACTION97.94
1.57-1.610.34561520.30987652X-RAY DIFFRACTION97.83
1.61-1.660.31791350.2717523X-RAY DIFFRACTION96.36
1.66-1.710.28561500.23757638X-RAY DIFFRACTION99.01
1.71-1.770.2571450.2287782X-RAY DIFFRACTION99.34
1.77-1.840.2431380.23117769X-RAY DIFFRACTION99.33
1.84-1.930.24821490.23167697X-RAY DIFFRACTION98.82
1.93-2.030.26881430.21577746X-RAY DIFFRACTION99.08
2.03-2.160.25221430.20897700X-RAY DIFFRACTION98.6
2.16-2.320.24311370.21017623X-RAY DIFFRACTION97.27
2.32-2.560.23451510.21087651X-RAY DIFFRACTION98.36
2.56-2.930.2211360.21797713X-RAY DIFFRACTION98.22
2.93-3.690.20411390.20647651X-RAY DIFFRACTION97.17
3.69-48.040.22251480.21427653X-RAY DIFFRACTION96.43

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