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- PDB-5jr3: Crystal structure of carminomycin-4-O-methyltransferase DnrK in c... -

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Basic information

Entry
Database: PDB / ID: 5jr3
TitleCrystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 4-methylumbelliferone
ComponentsCarminomycin 4-O-methyltransferase DnrK
KeywordsTRANSFERASE / natural product biosynthesis / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
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
7-hydroxy-4-methyl-2H-chromen-2-one / S-ADENOSYL-L-HOMOCYSTEINE / Carminomycin 4-O-methyltransferase DnrK
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWang, F. / Johnson, B.R. / Huber, T.D. / Singh, S. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM098248 United States
CitationJournal: To Be Published
Title: Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 4-methylumbelliferone (to be published)
Authors: Wang, F. / Johnson, B.R. / Huber, T.D. / Singh, S. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_fragment / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Oct 25, 2023Group: 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
B: Carminomycin 4-O-methyltransferase DnrK
C: Carminomycin 4-O-methyltransferase DnrK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,83621
Polymers123,0013
Non-polymers2,83418
Water15,043835
1
A: Carminomycin 4-O-methyltransferase DnrK
hetero molecules

A: Carminomycin 4-O-methyltransferase DnrK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,89014
Polymers82,0012
Non-polymers1,89012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area8380 Å2
ΔGint-139 kcal/mol
Surface area27010 Å2
MethodPISA
2
B: Carminomycin 4-O-methyltransferase DnrK
C: Carminomycin 4-O-methyltransferase DnrK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,89014
Polymers82,0012
Non-polymers1,89012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-150 kcal/mol
Surface area26850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.160, 111.098, 116.225
Angle α, β, γ (deg.)90.00, 120.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 41000.406 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius (bacteria) / Gene: dnrK / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q06528, carminomycin 4-O-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-4MU / 7-hydroxy-4-methyl-2H-chromen-2-one / 4-methylumbelliferone


Mass: 176.169 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C10H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.26M (NH4)SO4, 0.1M Tris pH 8.0, 0.2M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→48.635 Å / Num. obs: 225303 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2.06 % / Biso Wilson estimate: 21.73 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.92
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.84-1.960.3462.61198.4
1.96-2.090.2044.18199.5
2.09-2.260.1326.1199.5
2.26-2.470.0968.11199.3
2.47-2.770.07310.43199
2.77-3.190.05913.05198.8
3.19-3.910.0516.37198.2
3.91-5.510.04818.28197.7
5.51-48.6350.04818.64196.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEH

5eeh


Resolution: 1.84→48.632 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1801 1900 1.66 %
Rwork0.1595 --
obs0.1598 114398 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→48.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7934 0 177 835 8946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078382
X-RAY DIFFRACTIONf_angle_d0.9111450
X-RAY DIFFRACTIONf_dihedral_angle_d11.9835015
X-RAY DIFFRACTIONf_chiral_restr0.0571305
X-RAY DIFFRACTIONf_plane_restr0.0051491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.8860.27121370.23447682X-RAY DIFFRACTION95
1.886-1.9370.27921290.20777793X-RAY DIFFRACTION96
1.937-1.9940.25121310.19547929X-RAY DIFFRACTION97
1.994-2.05840.20431280.17867966X-RAY DIFFRACTION97
2.0584-2.1320.19881380.16927937X-RAY DIFFRACTION98
2.132-2.21730.20531330.16818057X-RAY DIFFRACTION99
2.2173-2.31820.17611400.1598031X-RAY DIFFRACTION99
2.3182-2.44050.20761360.16158108X-RAY DIFFRACTION99
2.4405-2.59340.19361380.15528116X-RAY DIFFRACTION99
2.5934-2.79360.16671420.1578097X-RAY DIFFRACTION100
2.7936-3.07470.17311360.15918159X-RAY DIFFRACTION100
3.0747-3.51950.16141380.15358147X-RAY DIFFRACTION100
3.5195-4.43370.14081380.13568206X-RAY DIFFRACTION100
4.4337-48.64870.17071360.1558270X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.65850.05410.68430.33380.03241.9140.0217-0.05980.01160.06040.0103-0.0622-0.20810.181-0.0070.1355-0.0270.02130.1169-0.01940.1595-48.6457-30.667714.0164
20.68060.32430.61990.6952-0.08151.52830.01160.0057-0.103-0.0980.08940.06610.1623-0.1295-0.10310.1628-0.06140.010.17150.03590.2115-21.4802-8.036517.0352
30.4587-0.27680.18491.3823-1.30781.6216-0.0214-0.1642-0.04020.5639-0.1043-0.1226-0.45190.1583-0.06530.3888-0.1226-0.04290.27830.05020.2058-4.47570.494449.5095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 11 through 402)
2X-RAY DIFFRACTION2(chain 'B' and resid 13 through 402)
3X-RAY DIFFRACTION3(chain 'C' and resid 10 through 402)

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