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- PDB-5c77: A novel protein arginine methyltransferase -

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Basic information

Entry
Database: PDB / ID: 5c77
TitleA novel protein arginine methyltransferase
ComponentsProtein arginine N-methyltransferase SFM1
KeywordsTRANSFERASE / protein arginine methyltransferase / SAH / Arginine / Yeast
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: 2.5 Å
AuthorsLv, F. / Zhang, T. / Ding, J.
CitationJournal: Cell Discov / Year: 2015
Title: Structural basis for Sfm1 functioning as a protein arginine methyltransferase.
Authors: Lv, F. / Zhang, T. / Zhou, Z. / Gao, S. / Wong, C.C. / Zhou, J.Q. / Ding, J.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
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
B: Protein arginine N-methyltransferase SFM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4644
Polymers51,6952
Non-polymers7692
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.375, 95.620, 58.407
Angle α, β, γ (deg.)90.00, 106.20, 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: 25847.664 Da / Num. of mol.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate (pH 6.5), 30% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15852 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 14.9

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Processing

SoftwareName: PHENIX / Version: 1.7.2_869 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C74

5c74


Resolution: 2.5→30.249 Å / SU ML: 0.83 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 789 4.98 %
Rwork0.2109 --
obs0.2136 15852 99.32 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.159 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5463 Å20 Å25.082 Å2
2--7.3558 Å2-0 Å2
3----5.0987 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 0 77 3426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063416
X-RAY DIFFRACTIONf_angle_d0.9974610
X-RAY DIFFRACTIONf_dihedral_angle_d16.2991344
X-RAY DIFFRACTIONf_chiral_restr0.064516
X-RAY DIFFRACTIONf_plane_restr0.004585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4971-2.65340.36861340.28862439X-RAY DIFFRACTION98
2.6534-2.85820.34881270.26342524X-RAY DIFFRACTION100
2.8582-3.14550.31891180.24862527X-RAY DIFFRACTION100
3.1455-3.60010.28341490.22072506X-RAY DIFFRACTION100
3.6001-4.53320.21281320.17642514X-RAY DIFFRACTION100
4.5332-30.25110.24291290.19062531X-RAY DIFFRACTION99

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