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- PDB-5h5d: The crystal structure of the yeast arginine methyltransferase SFM... -

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Basic information

Entry
Database: PDB / ID: 5h5d
TitleThe crystal structure of the yeast arginine methyltransferase SFM1 complexed with MTA
ComponentsProtein arginine N-methyltransferase SFM1
KeywordsTRANSFERASE / arginine methyltransferase / spout fold
Function / homologyProtein arginine N-methyltransferase SFM1-like / Protein arginine N-methyltransferase SFM1-like / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine methylation / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Protein arginine N-methyltransferase SFM1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsXie, W. / Wang, C. / Zeng, J.
CitationJournal: FEBS Lett. / Year: 2017
Title: A flexible cofactor-binding loop in the novel arginine methyltransferase Sfm1.
Authors: Wang, C. / Zeng, J. / Xie, W.
History
DepositionNov 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Protein arginine N-methyltransferase SFM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4452
Polymers27,1481
Non-polymers2971
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.527, 57.770, 43.153
Angle α, β, γ (deg.)90.00, 106.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein arginine N-methyltransferase SFM1 / SPOUT family methyltransferase 1


Mass: 27148.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SFM1, YOR021C, OR26.11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q12314, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.7 Å3/Da / Density % sol: 27.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M NaCl, 0.1 M Tris-HCl (pH 8.5), 38% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 5087 / % possible obs: 95.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.816 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C77

5c77


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.866 / SU B: 18.685 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28217 234 4.8 %RANDOM
Rwork0.22955 ---
obs0.23216 4608 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.406 Å2
Baniso -1Baniso -2Baniso -3
1--4.27 Å20 Å2-0.85 Å2
2--7.41 Å20 Å2
3----2.25 Å2
Refinement stepCycle: 1 / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 20 5 1512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021536
X-RAY DIFFRACTIONr_bond_other_d0.0070.021396
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9982092
X-RAY DIFFRACTIONr_angle_other_deg0.96733196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50124.47867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70215237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.579159
X-RAY DIFFRACTIONr_chiral_restr0.0660.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211727
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02331
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_it3.235.992777
X-RAY DIFFRACTIONr_mcbond_other3.2155.991776
X-RAY DIFFRACTIONr_mcangle_it4.7818.986966
X-RAY DIFFRACTIONr_mcangle_other4.7798.987967
X-RAY DIFFRACTIONr_scbond_it3.7646.143759
X-RAY DIFFRACTIONr_scbond_other3.7616.143760
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6429.121127
X-RAY DIFFRACTIONr_long_range_B_refined7.25647.551659
X-RAY DIFFRACTIONr_long_range_B_other7.25447.5541660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.697→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 14 -
Rwork0.242 303 -
obs--82.77 %

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