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- PDB-5m58: Crystal structure of CouO, a C-methyltransferase from Streptomyce... -

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Basic information

Entry
Database: PDB / ID: 5m58
TitleCrystal structure of CouO, a C-methyltransferase from Streptomyces rishiriensis
ComponentsC-methyltransferase CouO
KeywordsTRANSFERASE / C-methyltransferase / CouO / Friedel-Craft alkylation / SAM / transfrease
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / antibiotic biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / C-methyltransferase CouO
Function and homology information
Biological speciesStreptomyces rishiriensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPavkov-Keller, T. / Gruber, K.
Citation
Journal: PLoS ONE / Year: 2017
Title: Crystal Structure and Catalytic Mechanism of CouO, a Versatile C-Methyltransferase from Streptomyces rishiriensis.
Authors: Pavkov-Keller, T. / Steiner, K. / Faber, M. / Tengg, M. / Schwab, H. / Gruber-Khadjawi, M. / Gruber, K.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012
Title: Crystallization of the novel S-adenosyl-L-methionine-dependent C-methyltransferase CouO from Streptomyces rishiriensis and preliminary diffraction data analysis.
Authors: Lyskowski, A. / Tengg, M. / Steinkellner, G. / Schwab, H. / Gruber-Khadjawi, M. / Gruber, K.
History
DepositionOct 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-methyltransferase CouO
B: C-methyltransferase CouO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1294
Polymers51,3602
Non-polymers7692
Water5,657314
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint2 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.070, 82.950, 76.880
Angle α, β, γ (deg.)90.00, 96.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C-methyltransferase CouO / Coumermycin biosynthesis protein O


Mass: 25680.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rishiriensis (bacteria) / Gene: couO / Production host: Escherichia coli (E. coli)
References: UniProt: Q9F8T9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 2.3 mg/ml CouO 12.5%(w/v) PEG 1000, 12.5%(w/v) PEG 3350, 12.5%(v/v) MPD, 0.03 M of each halide (sodium fluoride, sodium bromide and sodium iodide), 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.0507 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0507 Å / Relative weight: 1
ReflectionResolution: 2.05→40.98 Å / Num. all: 87179 / Num. obs: 25206 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 10510 / Num. unique all: 3498 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.869 / SU B: 6.833 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.225 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26448 1306 5.1 %RANDOM
Rwork0.20345 ---
obs0.20662 24235 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.234 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.24 Å2
2---1.58 Å20 Å2
3---1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 52 314 3973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193753
X-RAY DIFFRACTIONr_bond_other_d0.0020.023509
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9665086
X-RAY DIFFRACTIONr_angle_other_deg0.95238036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3215459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70522.941187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03915600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7911538
X-RAY DIFFRACTIONr_chiral_restr0.0690.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214285
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02909
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.222.0831845
X-RAY DIFFRACTIONr_mcbond_other1.222.0841844
X-RAY DIFFRACTIONr_mcangle_it2.0763.122301
X-RAY DIFFRACTIONr_mcangle_other2.0763.1192302
X-RAY DIFFRACTIONr_scbond_it1.2972.2981908
X-RAY DIFFRACTIONr_scbond_other1.2972.2991908
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.163.3592786
X-RAY DIFFRACTIONr_long_range_B_refined4.67225.6484441
X-RAY DIFFRACTIONr_long_range_B_other4.67225.6464442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 101 -
Rwork0.293 1678 -
obs--91.7 %

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