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- PDB-5h5e: The crystal structure of the yeast arginine methyltransferase SFM... -

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Basic information

Entry
Database: PDB / ID: 5h5e
TitleThe crystal structure of the yeast arginine methyltransferase SFM1 complexed with SAH
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-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase SFM1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 1.2Nov 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)27,5332
Polymers27,1481
Non-polymers3841
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.731, 58.035, 43.357
Angle α, β, γ (deg.)90.00, 106.40, 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.72 Å3/Da / Density % sol: 28.57 %
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: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 10918 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 23.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.84 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C77

5c77


Resolution: 2.09→37.155 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 495 4.55 %
Rwork0.1911 --
obs0.1935 10868 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→37.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 26 47 1777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061769
X-RAY DIFFRACTIONf_angle_d0.8652397
X-RAY DIFFRACTIONf_dihedral_angle_d13.6571067
X-RAY DIFFRACTIONf_chiral_restr0.053270
X-RAY DIFFRACTIONf_plane_restr0.005306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0899-2.30020.27221270.22182487X-RAY DIFFRACTION95
2.3002-2.6330.24981220.22312610X-RAY DIFFRACTION100
2.633-3.3170.28511300.21292624X-RAY DIFFRACTION100
3.317-37.16050.21821160.16512652X-RAY DIFFRACTION99

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