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- PDB-5ful: Crystal Structure of Mus musculus Protein Arginine Methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 5ful
TitleCrystal Structure of Mus musculus Protein Arginine Methyltransferase 2 with SAH
ComponentsPROTEIN ARGININE N-METHYLTRANSFERASE 2
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE / S-ADENOSYL-L-HOMOCYSTEINE
Function / homology
Function and homology information


protein-arginine N-methyltransferase activity / methylation
Similarity search - Function
Methyltransferase small domain / Methyltransferase small domain / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / SH3 domain / Distorted Sandwich / Src homology 3 domains ...Methyltransferase small domain / Methyltransferase small domain / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / SH3 domain / Distorted Sandwich / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsCura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.
CitationJournal: FEBS J. / Year: 2017
Title: Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors.
Authors: Cura, V. / Marechal, N. / Troffer-Charlier, N. / Strub, J.M. / van Haren, M.J. / Martin, N.I. / Cianferani, S. / Bonnefond, L. / Cavarelli, J.
History
DepositionJan 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Jan 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_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.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_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN ARGININE N-METHYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4558
Polymers50,6361
Non-polymers8187
Water5,567309
1
A: PROTEIN ARGININE N-METHYLTRANSFERASE 2
hetero molecules

A: PROTEIN ARGININE N-METHYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,90916
Polymers101,2732
Non-polymers1,63714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5450 Å2
ΔGint-69.7 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.507, 115.414, 132.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2116-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN ARGININE N-METHYLTRANSFERASE 2


Mass: 50636.277 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q3UKX1, EC: 2.1.1.125

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Non-polymers , 6 types, 316 molecules

#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsG0 COMES FROM THE TEV CLEAVAGE SITE. MUTATION R445W

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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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 7 / Details: 16% PEG6000, 100MM CACL2, 100MM HEPES PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.89→43.6 Å / Num. obs: 40535 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.9
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.2 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FUB

5fub


Resolution: 1.89→43.26 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 19.91 / Stereochemistry target values: ML / Details: RESIDUES 1-106 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.1924 2030 5 %
Rwork0.1657 --
obs0.167 40528 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 1.89→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 50 309 3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192856
X-RAY DIFFRACTIONf_angle_d1.2893868
X-RAY DIFFRACTIONf_dihedral_angle_d12.0151662
X-RAY DIFFRACTIONf_chiral_restr0.088434
X-RAY DIFFRACTIONf_plane_restr0.009483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8915-1.93550.29641360.29552462X-RAY DIFFRACTION97
1.9355-1.98390.2661210.25532536X-RAY DIFFRACTION100
1.9839-2.03750.28751420.23512537X-RAY DIFFRACTION100
2.0375-2.09750.24631300.21852544X-RAY DIFFRACTION100
2.0975-2.16520.2381380.21162534X-RAY DIFFRACTION100
2.1652-2.24250.22241270.18782547X-RAY DIFFRACTION100
2.2425-2.33230.19681520.17322551X-RAY DIFFRACTION100
2.3323-2.43850.2211320.16452554X-RAY DIFFRACTION100
2.4385-2.5670.18891230.16152580X-RAY DIFFRACTION100
2.567-2.72780.20441330.16982571X-RAY DIFFRACTION100
2.7278-2.93840.19891320.16892551X-RAY DIFFRACTION100
2.9384-3.2340.18381330.16682597X-RAY DIFFRACTION100
3.234-3.70180.18961510.15242593X-RAY DIFFRACTION100
3.7018-4.6630.13751300.13392617X-RAY DIFFRACTION100
4.663-43.27080.19311500.15482724X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8716-0.35450.57482.0152-0.15811.5808-0.06410.10830.14780.0414-0.0092-0.0746-0.160.1810.07170.2407-0.00620.01660.2395-0.00280.2435-19.25713.2895-23.0136
20.67340.058-0.96390.3652-1.10724.2463-0.0272-0.06720.046-0.0154-0.0575-0.17280.22880.14090.0970.33640.02790.03110.2748-0.0430.3502-10.3087-15.8957-2.2169
30.5625-0.3970.46772.2735-0.64660.46330.07570.1741-0.059-0.2582-0.1584-0.19620.2270.18760.08560.29940.07260.05230.3206-0.03060.2662-11.2912-10.5526-21.3996
46.8083-4.5615-0.8713.13830.7482.4263-0.16260.0563-0.62850.387-0.04630.57830.25170.05770.35620.32660.01820.03790.2622-0.01760.3354-13.5892-23.6902-15.1284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 107 THROUGH 255 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 256 THROUGH 307 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 308 THROUGH 426 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 427 THROUGH 445 )

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