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- PDB-5fqo: Crystal structure of M. musculus protein arginine methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 5fqo
TitleCrystal structure of M. musculus protein arginine methyltransferase PRMT6 with SAH and magnesium
ComponentsPROTEIN ARGININE N-METHYLTRANSFERASE 6
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / 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 ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H3R2 methyltransferase activity / 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 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 / methylation / 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
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 6
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsBonnefond, L. / Cavarelli, J.
CitationJournal: To be Published
Title: Crystal Strcutures of Prmt6 in Complex with Sah in Alternative Conformations
Authors: Bonnefond, L. / Cura, V. / Troffer-Charlier, N. / Cavarelli, J.
History
DepositionDec 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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)44,7653
Polymers44,3561
Non-polymers4092
Water4,468248
1
A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules

A: PROTEIN ARGININE N-METHYLTRANSFERASE 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5296
Polymers88,7122
Non-polymers8174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area4690 Å2
ΔGint-59 kcal/mol
Surface area26720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.620, 78.620, 118.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-2074-

HOH

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Components

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


Mass: 44355.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PNEA-VH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6NZB1, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsL315F NATURAL VARIANT

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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: 2.06 Å3/Da / Density % sol: 40.29 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS PH 8.0 200 MM MGCL2 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178
DetectorType: DECTRIS PILATUS 3K / Detector: PIXEL / Date: Mar 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→40.5 Å / Num. obs: 27171 / % possible obs: 96.4 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 20.14 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.8 / % possible all: 84.4

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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 4C08

4c08


Resolution: 1.899→33.702 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 1358 5 %
Rwork0.1581 --
obs0.1601 27171 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.59 Å2
Refinement stepCycle: LAST / Resolution: 1.899→33.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 27 248 2824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112650
X-RAY DIFFRACTIONf_angle_d1.1313605
X-RAY DIFFRACTIONf_dihedral_angle_d12.9621580
X-RAY DIFFRACTIONf_chiral_restr0.073400
X-RAY DIFFRACTIONf_plane_restr0.007461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.96690.23841240.18322397X-RAY DIFFRACTION89
1.9669-2.04560.23131370.16932568X-RAY DIFFRACTION97
2.0456-2.13870.19491380.15832589X-RAY DIFFRACTION96
2.1387-2.25140.21351370.15712568X-RAY DIFFRACTION96
2.2514-2.39250.23071330.16472533X-RAY DIFFRACTION95
2.3925-2.57710.22231380.17882558X-RAY DIFFRACTION96
2.5771-2.83630.19511340.17572641X-RAY DIFFRACTION98
2.8363-3.24650.22691390.17062641X-RAY DIFFRACTION98
3.2465-4.08910.18521410.14462673X-RAY DIFFRACTION99
4.0891-33.70720.15751370.13932645X-RAY DIFFRACTION97

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