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- PDB-7pgj: Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions f... -

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Basic information

Entry
Database: PDB / ID: 7pgj
TitleChimeric carminomycin-4-O-methyltransferase (DnrK) with regions from 10-decarboxylate TamK and 10-hydroxylase RdmB, together with a single point mutation F297G
ComponentsCarminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
KeywordsBIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / aclacinomycin 10-hydroxylase / tsukubarubicin 10-decarboxylase
Function / homology
Function and homology information


carminomycin 4-O-methyltransferase / daunorubicin biosynthetic process / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / O-methyltransferase activity / antibiotic biosynthetic process / methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / 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 / Chem-ZBX / Methyltransferase domain-containing protein / Carminomycin 4-O-methyltransferase DnrK / Aclacinomycin 10-hydroxylase RdmB
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
Streptomyces tsukubensis (bacteria)
Streptomyces purpurascens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsDinis, 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 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 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

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Assembly

Deposited unit
A: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7213
Polymers39,9101
Non-polymers8112
Water4,702261
1
A: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
hetero molecules

A: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4426
Polymers79,8212
Non-polymers1,6224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5310 Å2
ΔGint-49 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.750, 124.950, 102.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-739-

HOH

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Components

#1: Protein Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB / COMT / Anthracycline 4-O-methyltransferase / O-methyltransferase / 15-demethoxy-epsilon-rhodomycin ...COMT / Anthracycline 4-O-methyltransferase / O-methyltransferase / 15-demethoxy-epsilon-rhodomycin 10-hydroxylase / 15-demethoxyaclacinomycin T


Mass: 39910.328 Da / Num. of mol.: 1
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. exp.) Streptomyces purpurascens (bacteria)
Gene: dnrK, STSU_011780, STSU_11775, rdmB / Strain: DSM 42081 / NBRC 108919 / NRRL 18488 / 9993 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q06528, UniProt: I2N5E8, UniProt: Q54527, carminomycin 4-O-methyltransferase, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: 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
#3: Chemical ChemComp-ZBX / methyl (1R,2R,4S)-2-ethyl-7-methoxy-2,4,5-tris(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1H-tetracene-1-carboxylate


Mass: 426.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: in 0.1 M Sodium acetate, pH 4.6; 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.13→62.5 Å / Num. obs: 22162 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.32 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.4
Reflection shellResolution: 2.13→2.21 Å / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 13.4 / Num. unique obs: 2165 / % possible all: 100

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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: 2.13→53.32 Å / SU ML: 0.1907 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.1634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 1133 5.11 %
Rwork0.1656 21027 -
obs0.1682 22160 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.75 Å2
Refinement stepCycle: LAST / Resolution: 2.13→53.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 57 261 2833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762641
X-RAY DIFFRACTIONf_angle_d0.92243614
X-RAY DIFFRACTIONf_chiral_restr0.0565426
X-RAY DIFFRACTIONf_plane_restr0.0099463
X-RAY DIFFRACTIONf_dihedral_angle_d13.7382951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.230.23951470.16542571X-RAY DIFFRACTION100
2.23-2.340.23311570.16542588X-RAY DIFFRACTION100
2.34-2.490.23561410.1622600X-RAY DIFFRACTION100
2.49-2.680.21761380.16992601X-RAY DIFFRACTION99.96
2.68-2.950.23631550.18012587X-RAY DIFFRACTION100
2.95-3.380.19911310.17652653X-RAY DIFFRACTION100
3.38-4.260.20441300.15322656X-RAY DIFFRACTION99.79
4.26-53.320.20641340.1622771X-RAY DIFFRACTION99.38

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