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- PDB-6m82: Crystal structure of TylM1 Y14paF bound to SAH and dTDP-phenol -

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Basic information

Entry
Database: PDB / ID: 6m82
TitleCrystal structure of TylM1 Y14paF 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 / antibiotic biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / 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: 1.3971 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

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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)29,4624
Polymers28,5371
Non-polymers9253
Water4,378243
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)58,9238
Polymers57,0742
Non-polymers1,8506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1790 Å2
ΔGint-15 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.556, 91.574, 93.386
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-624-

HOH

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Components

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


Mass: 28536.896 Da / Num. of mol.: 1 / Mutation: Y14paF
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): BL21-AI with pDULE2 paF plasmid
References: UniProt: P95748, dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 49.14 % / Mosaicity: 0.464 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Precipitant: 23% w/v PEG 3350, 20 mM sodium malonate, 1% v/v 2-propanol, 4.5 mM trimethylamine, 100 mM Hepes pH 7.3 Protein:20 mM sodium malonate pH 7.0, 100 mM sodium chloride, 5 mM AdoMet, ...Details: Precipitant: 23% w/v PEG 3350, 20 mM sodium malonate, 1% v/v 2-propanol, 4.5 mM trimethylamine, 100 mM Hepes pH 7.3 Protein:20 mM sodium malonate pH 7.0, 100 mM sodium chloride, 5 mM AdoMet, 5 mM dTDP-phenol, 12 mg/mL TylM1 Y14paF 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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / 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: 1.3971→50 Å / Num. obs: 53915 / % possible obs: 98.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 17.58 Å2 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.01 / Rrim(I) all: 0.039 / Χ2: 1.052 / Net I/σ(I): 19.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.433.40.57525960.7330.3160.6630.85776
1.43-1.466.40.48332360.870.1940.5230.9495.8
1.46-1.59.90.39433660.9470.130.4160.99499.4
1.5-1.5412.30.29634070.9780.0870.3091.051100
1.54-1.5914.20.23334120.9870.0640.2421.081100
1.59-1.6414.50.18533750.9930.050.1911.114100
1.64-1.714.60.14434470.9950.0390.1491.117100
1.7-1.7614.70.11533830.9970.0310.1191.084100
1.76-1.8414.70.0934100.9980.0240.0931.109100
1.84-1.9414.70.06834080.9990.0180.0711.06100
1.94-2.0614.80.05734300.9990.0150.0590.963100
2.06-2.2214.80.04834540.9990.0130.0491.018100
2.22-2.4514.80.04334420.9990.0120.0451.024100
2.45-2.814.70.03934730.9990.0110.0411.053100
2.8-3.5314.60.029349510.0080.031.085100
3.53-5013.60.023358110.0060.0231.02998.6

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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: 1.3971→34.967 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.89
RfactorNum. reflection% reflection
Rfree0.1725 2700 5.01 %
Rwork0.1491 --
obs0.1503 53913 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.69 Å2 / Biso mean: 24.2216 Å2 / Biso min: 8.44 Å2
Refinement stepCycle: final / Resolution: 1.3971→34.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 61 243 2081
Biso mean--27.56 38.54 -
Num. residues----237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3971-1.42250.3399920.35241899199170
1.4225-1.44980.34091400.26832501264192
1.4498-1.47940.25651430.19622701284499
1.4794-1.51160.22751440.145327012845100
1.5116-1.54680.17581450.124527292874100
1.5468-1.58540.16081450.118527552900100
1.5854-1.62830.15561400.120327122852100
1.6283-1.67620.18531410.119727342875100
1.6762-1.73030.17521500.12227462896100
1.7303-1.79220.15421450.124827282873100
1.7922-1.86390.15521450.124527352880100
1.8639-1.94870.13741420.114527422884100
1.9487-2.05150.16171440.119727582902100
2.0515-2.180.16771460.128227522898100
2.18-2.34830.15611450.139127622907100
2.3483-2.58450.18061460.150127802926100
2.5845-2.95830.18241480.160627792927100
2.9583-3.72650.14971490.158728112960100
3.7265-34.97790.18381500.16852888303898

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