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- PDB-4wxh: Carminomycin-4-O-methyltransferase (DnrK) variant (298Ser insert)... -

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Basic information

Entry
Database: PDB / ID: 4wxh
TitleCarminomycin-4-O-methyltransferase (DnrK) variant (298Ser insert) in complex with S-adenosyl-L-homocysteine (SAH) and aclacinomycin T
ComponentsCarminomycin 4-O-methyltransferase DnrK
KeywordsTRANSFERASE / methyltransferase / mono-oxygenase / SAH binding / antibiotic binding
Function / homology
Function and homology information


carminomycin 4-O-methyltransferase / daunorubicin biosynthetic process / O-methyltransferase activity / methyltransferase activity / methylation
Similarity search - Function
Helix Hairpins - #1350 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Helix Hairpins - #1350 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3VL / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / S-ADENOSYL-L-HOMOCYSTEINE / Carminomycin 4-O-methyltransferase DnrK
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMetsa-Ketela, M. / Niiranen, L.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland136060 Finland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Divergent evolution of an atypical S-adenosyl-l-methionine-dependent monooxygenase involved in anthracycline biosynthesis.
Authors: Grocholski, T. / Dinis, P. / Niiranen, L. / Niemi, J. / Metsa-Ketela, M.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Feb 28, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Carminomycin 4-O-methyltransferase DnrK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,94012
Polymers80,3972
Non-polymers2,54310
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-96 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.803, 100.995, 62.398
Angle α, β, γ (deg.)90.00, 102.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carminomycin 4-O-methyltransferase DnrK / COMT / Anthracycline 4-O-methyltransferase


Mass: 40198.496 Da / Num. of mol.: 2 / Fragment: UNP residues 2-356
Source method: isolated from a genetically manipulated source
Details: 298S insert / Source: (gene. exp.) Streptomyces peucetius (bacteria) / Gene: dnrK / Plasmid: pBHBdeltaHis / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q06528, carminomycin 4-O-methyltransferase

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Non-polymers , 5 types, 353 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: 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
#4: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 0.1 M BisTris, 24% PEG3350, 0.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9751 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2014
RadiationMonochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9751 Å / Relative weight: 1
ReflectionResolution: 1.9→52.1 Å / Num. obs: 55954 / % possible obs: 96.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.961 Å2 / Rsym value: 0.139 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.2 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XSCALEdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TW3

1tw3


Resolution: 1.9→52.168 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 2833 5.07 %random selection
Rwork0.1932 ---
obs0.1952 55913 96.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→52.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5284 0 167 343 5794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095631
X-RAY DIFFRACTIONf_angle_d1.3187703
X-RAY DIFFRACTIONf_dihedral_angle_d15.0752070
X-RAY DIFFRACTIONf_chiral_restr0.087892
X-RAY DIFFRACTIONf_plane_restr0.007992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93280.35841410.32352606X-RAY DIFFRACTION96
1.9328-1.96790.36431370.3332599X-RAY DIFFRACTION95
1.9679-2.00580.39811320.34842633X-RAY DIFFRACTION96
2.0058-2.04670.35781520.33372579X-RAY DIFFRACTION95
2.0467-2.09120.35151340.31322617X-RAY DIFFRACTION95
2.0912-2.13990.38351290.28892605X-RAY DIFFRACTION95
2.1399-2.19340.29051410.23542559X-RAY DIFFRACTION94
2.1934-2.25270.2551510.20642647X-RAY DIFFRACTION97
2.2527-2.3190.23731560.18982663X-RAY DIFFRACTION98
2.319-2.39380.21491300.17882724X-RAY DIFFRACTION98
2.3938-2.47940.23781550.17342655X-RAY DIFFRACTION98
2.4794-2.57860.22431520.17982690X-RAY DIFFRACTION98
2.5786-2.6960.25021440.17372676X-RAY DIFFRACTION98
2.696-2.83810.24541320.17942662X-RAY DIFFRACTION96
2.8381-3.01590.22591470.17232686X-RAY DIFFRACTION98
3.0159-3.24880.21551520.17532683X-RAY DIFFRACTION98
3.2488-3.57560.20471390.16092704X-RAY DIFFRACTION98
3.5756-4.09290.18411320.15352652X-RAY DIFFRACTION95
4.0929-5.15580.16391460.15712709X-RAY DIFFRACTION98
5.1558-52.18750.20361310.18652731X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 15.2407 Å / Origin y: 0.0011 Å / Origin z: 14.366 Å
111213212223313233
T0.134 Å2-0.014 Å2-0.0045 Å2-0.1515 Å2-0.0026 Å2--0.1063 Å2
L0.7952 °2-0.8317 °20.0043 °2-1.449 °2-0.0342 °2--0.1338 °2
S-0.0656 Å °-0.0831 Å °0.01 Å °0.1685 Å °0.0562 Å °0.0048 Å °-0.0106 Å °-0.0035 Å °0.0104 Å °
Refinement TLS groupSelection details: all

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