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- PDB-7pg7: 10-decarboxylase TamK from Streptomyces tsukubaensis -

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Basic information

Entry
Database: PDB / ID: 7pg7
Title10-decarboxylase TamK from Streptomyces tsukubaensis
ComponentsMethyltransferase
KeywordsBIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / tsukubarubicin 10-decarboxylase
Function / homology
Function and homology information


O-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 / Methyltransferase
Similarity search - Component
Biological speciesStreptomyces tsukubensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsNji Wandi, B. / 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 13, 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

Downloads & links

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Assembly

Deposited unit
D: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2462
Polymers39,8621
Non-polymers3841
Water4,414245
1
D: Methyltransferase
hetero molecules

D: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4924
Polymers79,7242
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5610 Å2
ΔGint-46 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.835, 39.692, 97.977
Angle α, β, γ (deg.)90.000, 114.076, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11D-528-

HOH

21D-650-

HOH

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Components

#1: Protein Methyltransferase


Mass: 39861.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tsukubensis (bacteria) / Gene: B7R87_22010 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: A0A5H2ULK2
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.04M potassium phosphate monobasic, 16% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryocoolin / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.51→56.1 Å / Num. obs: 65700 / % possible obs: 96.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.12 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 15.4
Reflection shellResolution: 1.51→1.54 Å / Rmerge(I) obs: 0.693 / Num. unique obs: 2707

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Processing

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

1tw2


Resolution: 1.51→28.04 Å / SU ML: 0.1646 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.1057
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2211 3253 4.95 %
Rwork0.1993 62413 -
obs0.2003 65666 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.76 Å2
Refinement stepCycle: LAST / Resolution: 1.51→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 26 245 2734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672543
X-RAY DIFFRACTIONf_angle_d0.99063468
X-RAY DIFFRACTIONf_chiral_restr0.0621402
X-RAY DIFFRACTIONf_plane_restr0.0106454
X-RAY DIFFRACTIONf_dihedral_angle_d13.2675911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.34691170.33112189X-RAY DIFFRACTION78.09
1.53-1.560.33391390.32752464X-RAY DIFFRACTION89.73
1.56-1.580.30851260.31642745X-RAY DIFFRACTION97.09
1.58-1.610.31981430.29192710X-RAY DIFFRACTION97.51
1.61-1.640.2521570.26182691X-RAY DIFFRACTION97.43
1.64-1.670.28931430.25562699X-RAY DIFFRACTION97.2
1.67-1.710.25041540.2362726X-RAY DIFFRACTION97
1.71-1.740.25331310.23952725X-RAY DIFFRACTION96.88
1.74-1.780.21951280.22112697X-RAY DIFFRACTION97.48
1.78-1.830.24111680.21472715X-RAY DIFFRACTION97.86
1.83-1.880.21391410.2112755X-RAY DIFFRACTION98
1.88-1.930.2371320.20012721X-RAY DIFFRACTION98.21
1.93-1.990.21081650.20912783X-RAY DIFFRACTION98.37
1.99-2.070.22281490.20462734X-RAY DIFFRACTION98.33
2.07-2.150.20551360.20572762X-RAY DIFFRACTION98.04
2.15-2.250.20981300.20282786X-RAY DIFFRACTION98.41
2.25-2.370.22051320.20512767X-RAY DIFFRACTION98.47
2.37-2.510.24491440.20492769X-RAY DIFFRACTION97.95
2.51-2.710.21041320.21062796X-RAY DIFFRACTION98.55
2.71-2.980.21641610.19732764X-RAY DIFFRACTION98.62
2.98-3.410.21721430.18272814X-RAY DIFFRACTION98.57
3.41-4.290.18931530.16632796X-RAY DIFFRACTION97.81
4.29-28.040.22611290.18882805X-RAY DIFFRACTION94.65

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