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- PDB-3px2: Structure of TylM1 from Streptomyces fradiae H123N mutant in comp... -

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Basic information

Entry
Database: PDB / ID: 3px2
TitleStructure of TylM1 from Streptomyces fradiae H123N mutant in complex with SAH and dTDP-Quip3N
ComponentsN-methyltransferase
KeywordsTRANSFERASE / SAM binding / N / N-dimethyltransferase / dTDP-Quip3N binding
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
CAC2371-like domains / S-adenosyl-L-methionine-dependent methyltransferases / Methyltransferase domain 25 / Methyltransferase domain / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Chem-T3Q / dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHolden, H.M. / Carney, A.E.
CitationJournal: Biochemistry / Year: 2011
Title: Molecular Architecture of TylM1 from Streptomyces fradiae: An N,N-Dimethyltransferase Involved in the Production of dTDP-d-mycaminose .
Authors: Carney, A.E. / Holden, H.M.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-methyltransferase
D: N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7398
Polymers56,7512
Non-polymers1,9886
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-15 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.571, 40.703, 87.208
Angle α, β, γ (deg.)90.00, 117.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-methyltransferase


Mass: 28375.697 Da / Num. of mol.: 2 / Mutation: H123N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces fradiae (bacteria) / Strain: ATCC 19609 / Gene: tylM1, tylMI(orf3*) / Plasmid: pET31b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95748
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-T3Q / [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate / thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose


Mass: 547.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 5000 monomethyl-ether, 2% 1,4-dioxane, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 6, 2010 / Details: Montell
RadiationMonochromator: nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.65→77.1 Å / Num. all: 60958 / Num. obs: 60958 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 9.6
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.8 / Num. unique all: 8728 / Rsym value: 0.39 / % possible all: 83.4

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0066refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PFH

3pfh


Resolution: 1.65→77.05 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 2.472 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24458 3073 5 %RANDOM
Rwork0.19417 ---
all0.19669 60948 --
obs0.19669 60948 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.534 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.06 Å2
2--0.34 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.65→77.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 130 414 4202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213918
X-RAY DIFFRACTIONr_angle_refined_deg2.2861.9815339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37922.088182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81415571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2011540
X-RAY DIFFRACTIONr_chiral_restr0.2140.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213020
X-RAY DIFFRACTIONr_mcbond_it1.7591.52393
X-RAY DIFFRACTIONr_mcangle_it2.55423803
X-RAY DIFFRACTIONr_scbond_it4.03331462
X-RAY DIFFRACTIONr_scangle_it5.74.51431
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 184 -
Rwork0.313 3750 -
obs--81.92 %

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