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- PDB-6m81: Crystal structure of TylM1 Y14F bound to SAH and dTDP-phenol -

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Basic information

Entry
Database: PDB / ID: 6m81
TitleCrystal structure of TylM1 Y14F bound to SAH and dTDP-phenol
ComponentsdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
KeywordsTRANSFERASE / TylM1 / N-methyltransferase
Function / homology
Function and homology information


dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase / S-adenosylmethionine-dependent methyltransferase activity / antibiotic biosynthetic process / methylation / protein homodimerization activity
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Chem-TLO / dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.782 Å
AuthorsFick, R.J. / McDole, B.G. / Trievel, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1508492 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1.
Authors: Fick, R.J. / Horowitz, S. / McDole, B.G. / Clay, M.C. / Mehl, R.A. / Al-Hashimi, H.M. / Scheiner, S. / Trievel, R.C.
History
DepositionAug 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
B: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
C: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
D: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,53812
Polymers114,0884
Non-polymers3,4518
Water14,142785
1
A: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
hetero molecules

C: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7696
Polymers57,0442
Non-polymers1,7254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_848-x+3,y-1/2,-z+31
Buried area1560 Å2
ΔGint-18 kcal/mol
Surface area19110 Å2
MethodPISA
2
B: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
hetero molecules

D: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7696
Polymers57,0442
Non-polymers1,7254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_848-x+3,y-1/2,-z+31
Buried area1590 Å2
ΔGint-18 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.897, 92.353, 80.561
Angle α, β, γ (deg.)90.000, 106.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase / Tylosin biosynthesis protein M1


Mass: 28521.881 Da / Num. of mol.: 4 / Mutation: Y14F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: tylM1, tylMI / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P95748, dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-TLO / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine / thymidine diphosphate phenol


Mass: 478.284 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.31 Å3/Da / Density % sol: 46.78 % / Mosaicity: 0.487 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.46
Details: Precipitant:27% w/v PEG 3350, 20 mM sodium malonate, 1.25% v/v 2-propanol, 5.6 mM trimethylamine, 100 mM Hepes pH 7.46 Protein:20 mM sodium malonate pH 7.0, 100 mM sodium chloride, 5 mM ...Details: Precipitant:27% w/v PEG 3350, 20 mM sodium malonate, 1.25% v/v 2-propanol, 5.6 mM trimethylamine, 100 mM Hepes pH 7.46 Protein:20 mM sodium malonate pH 7.0, 100 mM sodium chloride, 5 mM AdoMet, 5 mM dTDP-phenol, 9 mg/mL TylM1 Y14F Protein:Precipitant 4:2uL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 96413 / % possible obs: 97.5 % / Redundancy: 7 % / Biso Wilson estimate: 22.61 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Χ2: 2.238 / Net I/σ(I): 14.9 / Num. measured all: 678249
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.824.60.30952850.950.1460.3430.91980.7
1.82-1.875.30.27160330.9660.1220.2981.01992.1
1.87-1.926.20.24663660.970.1040.2682.04396.9
1.92-1.976.90.19765210.9840.0790.2131.70699
1.97-2.047.40.15665570.9930.0610.1681.1499.9
2.04-2.117.50.14566020.9890.0560.1551.755100
2.11-2.197.70.11865250.9950.0450.1261.25100
2.19-2.297.50.11365870.9950.0440.1212.114100
2.29-2.427.70.09265690.9960.0350.0981.687100
2.42-2.577.70.08266070.9970.0320.0872.029100
2.57-2.777.60.0765620.9970.0270.0752.49199.9
2.77-3.047.60.06165970.9980.0240.0652.71100
3.04-3.487.60.05666210.9980.0220.063.75199.9
3.48-4.396.90.04865110.9980.020.0534.46998.4
4.39-506.60.03964700.9980.0160.0423.55396.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.782→36.956 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 4818 5 %
Rwork0.1751 91528 -
obs0.1769 96346 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.21 Å2 / Biso mean: 27.962 Å2 / Biso min: 12.85 Å2
Refinement stepCycle: final / Resolution: 1.782→36.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7154 0 228 785 8167
Biso mean--30.14 36.71 -
Num. residues----953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7824-1.80270.31171250.26592365249075
1.8027-1.82390.33751360.25172592272884
1.8239-1.84610.27831490.22542834298390
1.8461-1.86950.27781520.20492870302294
1.8695-1.89410.29321580.20063037319596
1.8941-1.920.21691590.19343024318397
1.92-1.94750.27911620.19153063322599
1.9475-1.97650.23671650.18643116328199
1.9765-2.00740.26611640.190231373301100
2.0074-2.04030.24421640.186930913255100
2.0403-2.07550.21561630.185431333296100
2.0755-2.11330.2341660.184831403306100
2.1133-2.15390.22521640.181231073271100
2.1539-2.19790.22461630.180331043267100
2.1979-2.24560.25921650.177231403305100
2.2456-2.29790.22491640.182331183282100
2.2979-2.35530.22071640.179631073271100
2.3553-2.4190.24711650.179331293294100
2.419-2.49020.2321650.181231463311100
2.4902-2.57050.21391660.176931433309100
2.5705-2.66240.2181640.17731143278100
2.6624-2.76890.21891640.179131173281100
2.7689-2.89490.22861670.185331553322100
2.8949-3.04750.21261630.191531153278100
3.0475-3.23830.25191650.194731333298100
3.2383-3.48810.21991670.175131623329100
3.4881-3.83880.1681640.16183111327599
3.8388-4.39360.16561620.1463080324298
4.3936-5.53240.14021590.1423024318396
5.5324-36.96390.19831640.16413121328597

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