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- PDB-4c08: Crystal structure of M. musculus protein arginine methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 4c08
TitleCrystal structure of M. musculus protein arginine methyltransferase PRMT6 with CaCl2 at 1.34 Angstroms
ComponentsPROTEIN ARGININE N-METHYLTRANSFERASE 6
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone H3 methyltransferase activity / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / protein modification process / cellular senescence / histone binding / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.338 Å
AuthorsBonnefond, L. / Cura, V. / Troffer-Charlier, N. / Mailliot, J. / Wurtz, J.M. / Cavarelli, J.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Functional Insights from High Resolution Structures of Mouse Protein Arginine Methyltransferase 6.
Authors: Bonnefond, L. / Stojko, J. / Mailliot, J. / Troffer-Charlier, N. / Cura, V. / Wurtz, J.M. / Cianferani, S. / Cavarelli, J.
History
DepositionJul 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7607
Polymers42,3221
Non-polymers4396
Water5,657314
1
A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules

A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,52114
Polymers84,6442
Non-polymers87712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area6070 Å2
ΔGint-116.5 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.325, 79.325, 118.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein PROTEIN ARGININE N-METHYLTRANSFERASE 6 / HISTONE-ARGININE N-METHYLTRANSFERASE PRMT6


Mass: 42321.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
References: UniProt: Q6NZB1, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.57 Å3/Da / Density % sol: 52.21 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS PH 8.0, 200 MM CACL2, 19% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.34→33.98 Å / Num. obs: 81559 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Biso Wilson estimate: 19.81 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.99
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.2 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y1W

2y1w


Resolution: 1.338→33.983 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 15.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1642 4077 5 %
Rwork0.1405 --
obs0.1417 81555 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.338→33.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 21 314 2888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082711
X-RAY DIFFRACTIONf_angle_d1.2323697
X-RAY DIFFRACTIONf_dihedral_angle_d13.4821020
X-RAY DIFFRACTIONf_chiral_restr0.076408
X-RAY DIFFRACTIONf_plane_restr0.006478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3382-1.35390.39561220.30022310X-RAY DIFFRACTION87
1.3539-1.37050.32851370.2782609X-RAY DIFFRACTION96
1.3705-1.38780.27821400.24792647X-RAY DIFFRACTION99
1.3878-1.40610.23021400.20212679X-RAY DIFFRACTION100
1.4061-1.42530.20711410.17872678X-RAY DIFFRACTION100
1.4253-1.44570.17941410.16632678X-RAY DIFFRACTION100
1.4457-1.46730.20011410.15252689X-RAY DIFFRACTION100
1.4673-1.49020.17141420.1492698X-RAY DIFFRACTION100
1.4902-1.51460.17611410.12792673X-RAY DIFFRACTION100
1.5146-1.54070.17581420.13682700X-RAY DIFFRACTION100
1.5407-1.56880.13321400.122664X-RAY DIFFRACTION100
1.5688-1.59890.15381420.11762696X-RAY DIFFRACTION100
1.5989-1.63160.13941410.11152670X-RAY DIFFRACTION100
1.6316-1.6670.14261400.10652674X-RAY DIFFRACTION100
1.667-1.70580.16451410.11332679X-RAY DIFFRACTION100
1.7058-1.74850.12831420.1152693X-RAY DIFFRACTION100
1.7485-1.79570.17681420.11512691X-RAY DIFFRACTION100
1.7957-1.84860.14861430.11882719X-RAY DIFFRACTION100
1.8486-1.90820.14261400.1182654X-RAY DIFFRACTION100
1.9082-1.97640.16191410.12072689X-RAY DIFFRACTION100
1.9764-2.05560.13591410.12172666X-RAY DIFFRACTION100
2.0556-2.14910.14381430.12232718X-RAY DIFFRACTION100
2.1491-2.26240.14931410.12222692X-RAY DIFFRACTION100
2.2624-2.40410.15211420.13152691X-RAY DIFFRACTION100
2.4041-2.58970.14841400.13652666X-RAY DIFFRACTION100
2.5897-2.85020.16941430.14862711X-RAY DIFFRACTION100
2.8502-3.26230.18411420.15962696X-RAY DIFFRACTION100
3.2623-4.1090.16671420.13852711X-RAY DIFFRACTION100
4.109-33.99380.16611440.15672737X-RAY DIFFRACTION100

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