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- PDB-6m83: Crystal structure of TylM1 S120A bound to SAH and dTDP-phenol -

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Basic information

Entry
Database: PDB / ID: 6m83
TitleCrystal structure of TylM1 S120A 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: 1.3685 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,4204
Polymers28,5221
Non-polymers8983
Water3,909217
1
A: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)58,8408
Polymers57,0442
Non-polymers1,7966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1800 Å2
ΔGint-33 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.521, 91.267, 93.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 28521.885 Da / Num. of mol.: 1 / Mutation: S120A
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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C16H20N2O11P2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.42 Å3/Da / Density % sol: 49.1 % / Mosaicity: 0.288 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: Precipitant:27% w/v PEG 3350, 20 mM sodium malonate, 1% v/v 2-propanol, 4.5 mM trimethylamine, 100 mM Hepes pH 7.7 Protein:20 mM sodium malonate pH 7.0, 100 mM sodium chloride, 5 mM AdoMet, ...Details: Precipitant:27% w/v PEG 3350, 20 mM sodium malonate, 1% v/v 2-propanol, 4.5 mM trimethylamine, 100 mM Hepes pH 7.7 Protein:20 mM sodium malonate pH 7.0, 100 mM sodium chloride, 5 mM AdoMet, 5 mM dTDP-phenol, 18 mg/mL TylM1 S120A 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: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.3685→50 Å / Num. obs: 57236 / % possible obs: 97.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 15.22 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.014 / Rrim(I) all: 0.051 / Χ2: 1.046 / Net I/σ(I): 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.37-1.43.20.42328060.8380.2320.4870.93177.3
1.4-1.435.10.41632870.8660.1850.4580.95691.7
1.43-1.4780.37235840.9460.1330.3960.99298.7
1.47-1.5110.80.32135830.9740.0990.3361.02699.9
1.51-1.5512.80.26536420.9870.0760.2761.067100
1.55-1.614.10.21736050.9910.060.2251.098100
1.6-1.6614.70.18136420.9940.0490.1871.112100
1.66-1.7314.80.14636130.9960.0390.1511.093100
1.73-1.814.80.1236380.9970.0320.1241.169100
1.8-1.914.80.08936460.9980.0240.0920.96100
1.9-2.0214.80.0736370.9980.0190.0720.95100
2.02-2.1714.80.05936500.9990.0160.0611.04100
2.17-2.3914.70.05536750.9990.0150.0571.074100
2.39-2.7414.40.04936740.9990.0130.0511.019100
2.74-3.4514.20.03737320.9990.010.0390.925100
3.45-5013.20.03238220.9990.0090.0331.12999

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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: 1.3685→34.995 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.49
RfactorNum. reflection% reflection
Rfree0.1817 2868 5.01 %
Rwork0.1527 --
obs0.1542 57233 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.42 Å2 / Biso mean: 21.3019 Å2 / Biso min: 8.55 Å2
Refinement stepCycle: final / Resolution: 1.3685→34.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 58 217 2070
Biso mean--17.89 32.88 -
Num. residues----237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3685-1.39210.2765990.25472039213874
1.3921-1.41740.27871420.21992409255189
1.4174-1.44460.26061340.18482628276296
1.4446-1.47410.22081430.15242751289499
1.4741-1.50620.16631440.131927342878100
1.5062-1.54120.17111440.123327752919100
1.5412-1.57980.16761450.124727632908100
1.5798-1.62250.18891490.123727362885100
1.6225-1.67020.1431470.118627582905100
1.6702-1.72410.15241410.119727612902100
1.7241-1.78580.18331470.123127652912100
1.7858-1.85730.14231460.132927592905100
1.8573-1.94180.15121520.12827622914100
1.9418-2.04410.18241420.136527862928100
2.0441-2.17220.17071430.145127732916100
2.1722-2.33990.17851490.15427932942100
2.3399-2.57530.19521450.164427882933100
2.5753-2.94780.19131510.173328272978100
2.9478-3.71320.18691480.165728282976100
3.7132-35.00650.18351570.1592930308799

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