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- PDB-5h5f: The crystal structure of the yeast arginine methyltransferase SFM... -

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Basic information

Entry
Database: PDB / ID: 5h5f
TitleThe crystal structure of the yeast arginine methyltransferase SFM1 complexed with SAM
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 / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / cytoplasm / S-ADENOSYLMETHIONINE / Protein arginine N-methyltransferase SFM1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsXie, W. / Wang, C. / Zeng, J.
Funding support China, 2items
OrganizationGrant numberCountry
Fundamental Research Funds for the Central Universities16lgjc76 China
the Science and Technology Program of Guangzhou201504010025 China
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)27,5472
Polymers27,1481
Non-polymers3981
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.712, 62.417, 44.695
Angle α, β, γ (deg.)90.00, 112.31, 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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.84 Å3/Da / Density % sol: 33.16 %
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 PILATUS3 S 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: 1.7→50 Å / Num. obs: 21761 / % possible obs: 95.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 24.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 9.6 / CC1/2: 0.974 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C77

5c77


Resolution: 1.7→34.471 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 16.63
RfactorNum. reflection% reflectionSelection details
Rfree0.1776 1044 5.03 %RANDOM
Rwork0.1536 ---
obs0.1548 20770 95.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 27 244 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091906
X-RAY DIFFRACTIONf_angle_d1.2562584
X-RAY DIFFRACTIONf_dihedral_angle_d14.4421149
X-RAY DIFFRACTIONf_chiral_restr0.093290
X-RAY DIFFRACTIONf_plane_restr0.007328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6995-1.78910.22341450.16262814X-RAY DIFFRACTION95
1.7891-1.90120.1961770.15322707X-RAY DIFFRACTION95
1.9012-2.04790.20171350.15272900X-RAY DIFFRACTION97
2.0479-2.2540.19051360.15792815X-RAY DIFFRACTION96
2.254-2.58010.19041670.16272838X-RAY DIFFRACTION97
2.5801-3.25020.18221480.16612827X-RAY DIFFRACTION96
3.2502-34.47790.14371360.1392825X-RAY DIFFRACTION94

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