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- PDB-5c74: Structure of a novel protein arginine methyltransferase -

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Basic information

Entry
Database: PDB / ID: 5c74
TitleStructure of a novel protein arginine methyltransferase
ComponentsProtein arginine N-methyltransferase SFM1
KeywordsTRANSFERASE / Protein arginine methyltransferase / Binging seites / S-Adenosylhomocysteine
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 / NICKEL (II) ION / Protein arginine N-methyltransferase SFM1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsLv, F. / 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)50,1488
Polymers49,7212
Non-polymers4276
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-64 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.570, 107.570, 87.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 24860.529 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M (NH4)2SO4, 0.1 M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 41006 / % possible obs: 99.8 % / Redundancy: 21.4 % / Net I/σ(I): 38.3
Reflection shellHighest resolution: 1.9 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.9→42.158 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 2056 5.02 %
Rwork0.1929 --
obs0.1949 40953 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→42.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 14 443 3393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073003
X-RAY DIFFRACTIONf_angle_d0.9984043
X-RAY DIFFRACTIONf_dihedral_angle_d14.0231153
X-RAY DIFFRACTIONf_chiral_restr0.042447
X-RAY DIFFRACTIONf_plane_restr0.005511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.94320.22721320.1872516X-RAY DIFFRACTION99
1.9432-1.99180.2141350.17892547X-RAY DIFFRACTION100
1.9918-2.04560.25471330.18712546X-RAY DIFFRACTION100
2.0456-2.10580.24651240.18832573X-RAY DIFFRACTION100
2.1058-2.17380.23521320.17912568X-RAY DIFFRACTION100
2.1738-2.25150.2381400.17812579X-RAY DIFFRACTION100
2.2515-2.34160.23121440.18992570X-RAY DIFFRACTION100
2.3416-2.44820.24071300.19792561X-RAY DIFFRACTION100
2.4482-2.57720.22631390.19042595X-RAY DIFFRACTION100
2.5772-2.73870.24451320.19532592X-RAY DIFFRACTION100
2.7387-2.95010.24621600.20022564X-RAY DIFFRACTION100
2.9501-3.24690.2331370.19612623X-RAY DIFFRACTION100
3.2469-3.71650.22631570.19092609X-RAY DIFFRACTION100
3.7165-4.68140.2161320.17672672X-RAY DIFFRACTION100
4.6814-42.16850.23541290.2192782X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 27.1769 Å / Origin y: 1.8963 Å / Origin z: -21.0808 Å
111213212223313233
T0.1562 Å2-0.004 Å2-0.0127 Å2-0.1231 Å20.0017 Å2--0.1562 Å2
L0.269 °2-0.0484 °20.0285 °2-1.3804 °2-0.3205 °2--0.472 °2
S0.0076 Å °-0.0055 Å °0.0399 Å °0.0733 Å °0.0288 Å °0.2453 Å °-0.1166 Å °-0.0582 Å °-0.028 Å °
Refinement TLS groupSelection details: all

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