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

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Basic information

Entry
Database: PDB / ID: 5fwd
TitleCrystal Structure of Mus musculus Protein Arginine Methyltransferase 2 with CP2
ComponentsPROTEIN ARGININE N-METHYLTRANSFERASE 2
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE
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. / SH3 domain / Vaccinia Virus protein VP39 / 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. / SH3 domain / Vaccinia Virus protein VP39 / 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
Chem-GJV / Protein arginine N-methyltransferase 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionFeb 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 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.ptnr1_symmetry / _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.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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,65612
Polymers50,6361
Non-polymers1,02011
Water4,828268
1
A: PROTEIN ARGININE N-METHYLTRANSFERASE 2
hetero molecules

A: PROTEIN ARGININE N-METHYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,31224
Polymers101,2732
Non-polymers2,03922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6590 Å2
ΔGint-34.8 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.964, 114.520, 132.085
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-1460-

CA

21A-2110-

HOH

31A-2267-

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, 279 molecules

#2: Chemical ChemComp-GJV / 9-(7-{[amino(iminio)methyl]amino}-5,6,7-trideoxy-beta-D-ribo-heptofuranosyl)-9H-purin-6-amine


Mass: 337.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 20% PEG6000, 100 MM HEPES PH7, 100MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→44 Å / Num. obs: 34118 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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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: 2→43.263 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 1710 5 %
Rwork0.1882 --
obs0.1893 34075 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.8 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Refinement stepCycle: LAST / Resolution: 2→43.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 64 268 3055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072857
X-RAY DIFFRACTIONf_angle_d0.6993873
X-RAY DIFFRACTIONf_dihedral_angle_d12.8881038
X-RAY DIFFRACTIONf_chiral_restr0.032433
X-RAY DIFFRACTIONf_plane_restr0.003498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05890.28861390.2842649X-RAY DIFFRACTION100
2.0589-2.12540.3021450.27282687X-RAY DIFFRACTION100
2.1254-2.20130.28011390.25842667X-RAY DIFFRACTION100
2.2013-2.28950.28651430.24482660X-RAY DIFFRACTION100
2.2895-2.39360.27421500.23162657X-RAY DIFFRACTION100
2.3936-2.51980.2671390.21562687X-RAY DIFFRACTION100
2.5198-2.67770.21941320.20652688X-RAY DIFFRACTION100
2.6777-2.88440.22361260.20022713X-RAY DIFFRACTION100
2.8844-3.17460.21731610.19862697X-RAY DIFFRACTION100
3.1746-3.63370.19781400.17072688X-RAY DIFFRACTION100
3.6337-4.57730.16031410.14112740X-RAY DIFFRACTION100
4.5773-43.27330.17011550.16062832X-RAY DIFFRACTION99
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)
11.8385-0.07080.092.0889-0.25421.1969-0.0501-0.01190.14350.0878-0.0043-0.0144-0.12610.10330.05220.20060.0003-0.00010.1973-0.01220.2234-19.50513.1848-22.8641
20.75450.5737-2.07070.7728-2.74568.4304-0.1364-0.11040.0267-0.0699-0.0667-0.14720.43890.13420.20080.30970.03130.03930.2424-0.04430.3448-10.3876-15.9422-2.0098
30.3693-0.18410.41992.2514-0.63940.3407-0.01870.1132-0.1099-0.177-0.0885-0.09450.18930.1110.11010.28820.04250.05850.3108-0.03080.2865-11.3283-10.5719-21.1242
46.31390.089-1.543.01170.75873.1422-0.40590.3741-1.1670.6043-0.08690.93030.2429-0.02750.46740.2635-0.00530.01710.22090.01210.1175-13.6698-23.7877-14.8739
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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