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

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Basic information

Entry
Database: PDB / ID: 5eeg
TitleCrystal structure of carminomycin-4-O-methyltransferase DnrK in complex with tetrazole-SAH
ComponentsCarminomycin 4-O-methyltransferase DnrK
KeywordsTRANSFERASE / unnatural substrate / 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
Chem-S8M / Carminomycin 4-O-methyltransferase DnrK
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.255 Å
AuthorsWang, F. / Singh, S. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM098248 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI52188 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Functional AdoMet Isosteres Resistant to Classical AdoMet Degradation Pathways.
Authors: Huber, T.D. / Wang, F. / Singh, S. / Johnson, B.R. / Zhang, J. / Sunkara, M. / Van Lanen, S.G. / Morris, A.J. / Phillips, G.N. / Thorson, J.S.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Sep 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 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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)82,8184
Polymers82,0012
Non-polymers8172
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-48 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.562, 104.180, 62.986
Angle α, β, γ (deg.)90.00, 105.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41000.406 Da / Num. of mol.: 2
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-S8M / (2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-[[(3~{S})-3-azanyl-3-(1~{H}-1,2,3,4-tetrazol-5-yl)propyl]sulfanylmethyl]oxolane-3,4-diol


Type: RNA linking / Mass: 408.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N10O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM magnesium formate dihydrate and 15% (w/v) PEG 3,350

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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: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 35379 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 18.03 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.072 / Rrim(I) all: 0.153 / Rsym value: 0.125 / Χ2: 0.648 / Net I/av σ(I): 7.886 / Net I/σ(I): 4.1 / Num. measured all: 153712
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.294.20.34617330.8870.1910.3970.64999.7
2.29-2.334.30.35818020.8880.1970.410.68199.9
2.33-2.384.40.32217530.910.1730.3660.6999.9
2.38-2.424.30.28817760.9330.1560.3290.69999.8
2.42-2.484.40.27617340.9450.1480.3130.69899.9
2.48-2.534.40.24817750.9460.1330.2820.70199.9
2.53-2.64.40.23717730.9540.1270.2690.6999.9
2.6-2.674.40.20717580.9650.1110.2360.684100
2.67-2.754.40.18817960.970.1020.2150.69799.8
2.75-2.834.40.18817510.9670.1010.2140.70399.9
2.83-2.944.40.16117530.9780.0860.1830.68199.8
2.94-3.054.40.13617800.9850.0730.1550.68199.9
3.05-3.194.40.12717870.9850.0680.1440.60399.8
3.19-3.364.40.11417740.9860.060.130.64799.8
3.36-3.574.40.10717640.9860.0560.1210.65799.7
3.57-3.854.40.10817500.9860.0570.1220.75999.4
3.85-4.234.30.09817590.9860.0510.1110.68898.8
4.23-4.844.20.08617530.9890.0460.0980.47397.7
4.84-6.094.30.0717920.9940.0370.0790.40799.3
6.09-304.30.08518160.9890.0470.0980.4799.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIX(phenix.refine: 1.9_1692)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TW2

1tw2


Resolution: 2.255→29.854 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 2013 5.69 %
Rwork0.1966 --
obs0.1995 35347 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.255→29.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 56 490 5683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085299
X-RAY DIFFRACTIONf_angle_d0.9597216
X-RAY DIFFRACTIONf_dihedral_angle_d20.1671914
X-RAY DIFFRACTIONf_chiral_restr0.063837
X-RAY DIFFRACTIONf_plane_restr0.005941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2545-2.31090.29831320.22212293X-RAY DIFFRACTION96
2.3109-2.37340.3241500.23022362X-RAY DIFFRACTION100
2.3734-2.44320.24611470.20772384X-RAY DIFFRACTION100
2.4432-2.5220.29061370.21892410X-RAY DIFFRACTION100
2.522-2.61210.27671550.22242371X-RAY DIFFRACTION100
2.6121-2.71660.31031330.22362378X-RAY DIFFRACTION100
2.7166-2.84010.31371460.22172389X-RAY DIFFRACTION100
2.8401-2.98970.26471380.21082405X-RAY DIFFRACTION100
2.9897-3.17690.28681430.20242384X-RAY DIFFRACTION100
3.1769-3.42180.23331510.18762368X-RAY DIFFRACTION100
3.4218-3.76560.22551450.17582418X-RAY DIFFRACTION100
3.7656-4.30910.18511410.16682373X-RAY DIFFRACTION99
4.3091-5.42370.20391460.17192360X-RAY DIFFRACTION98
5.4237-29.85680.21851490.19242439X-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)
13.1185-0.68940.47013.2035-0.42321.86950.08170.2754-0.4645-0.2304-0.0559-0.22130.14220.1758-0.01680.1294-0.00750.01820.1325-0.03380.2236-3.6934-11.4411-19.5806
22.8983-0.4376-0.40522.36840.58191.81550.11490.27410.1989-0.2836-0.08610.2558-0.1131-0.1401-0.03170.1290.004-0.0430.13080.02840.1609-26.63187.3778-19.4603
31.63110.8072-0.01191.8726-0.00780.5594-0.00130.16370.0458-0.09330.0284-0.1072-0.07330.0279-0.02650.09450.01070.00030.1636-0.00460.1204-2.327620.4987-11.7712
41.18030.5556-0.07081.95970.07420.7118-0.00050.0794-0.0866-0.12560.03120.00730.0929-0.0065-0.02340.10010.0129-0.02020.1222-0.00130.1143-28.0615-24.6337-11.8442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 15 through 101)
2X-RAY DIFFRACTION2(chain 'B' and resid 15 through 101)
3X-RAY DIFFRACTION3(chain 'A' and resid 102 through 352)
4X-RAY DIFFRACTION4(chain 'B' and resid 102 through 352)

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