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- PDB-8pjd: Crystal Structure of Mus musculus Protein Arginine Methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 8pjd
TitleCrystal Structure of Mus musculus Protein Arginine Methyltransferase 2 94-445
ComponentsProtein arginine N-methyltransferase 2
KeywordsTRANSFERASE / protein arginine N-methyltransferase / PRMT / SH3 / methylation / transcription
Function / homology
Function and homology information


type I protein arginine methyltransferase / protein-arginine N-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Methyltransferase small domain / Methyltransferase small domain / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Methyltransferase small domain / Methyltransferase small domain / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 94-445
Authors: Cura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J.
History
DepositionJun 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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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)41,2908
Polymers40,6231
Non-polymers6677
Water7,296405
1
A: Protein arginine N-methyltransferase 2
hetero molecules

A: Protein arginine N-methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,58016
Polymers81,2462
Non-polymers1,33314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5450 Å2
ΔGint-88 kcal/mol
Surface area28230 Å2
Unit cell
Length a, b, c (Å)65.052, 115.980, 133.718
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-748-

HOH

21A-1003-

HOH

31A-1005-

HOH

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Components

#1: Protein Protein arginine N-methyltransferase 2


Mass: 40623.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt2, Hrmt1l1
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q3UKX1
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: 1.3M AcONa pH5.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.6→29.25 Å / Num. obs: 65279 / % possible obs: 97.5 % / Redundancy: 7 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Rrim(I) all: 0.07845 / Net I/σ(I): 17.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.2 % / Rmerge(I) obs: 2.384 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2584 / CC1/2: 0.38 / CC star: 0.59 / Rpim(I) all: 0.808 / Rrim(I) all: 2.527 / % possible all: 77.85

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4958: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.25 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 3303 5.06 %
Rwork0.1714 --
obs0.1723 65234 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 44 405 3230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082896
X-RAY DIFFRACTIONf_angle_d1.0053941
X-RAY DIFFRACTIONf_dihedral_angle_d15.2911034
X-RAY DIFFRACTIONf_chiral_restr0.055441
X-RAY DIFFRACTIONf_plane_restr0.009500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.38221150.33322064X-RAY DIFFRACTION78
1.62-1.650.36981160.30682119X-RAY DIFFRACTION83
1.65-1.670.31031300.27582300X-RAY DIFFRACTION87
1.67-1.70.28341360.26142470X-RAY DIFFRACTION94
1.7-1.730.23081350.23632599X-RAY DIFFRACTION100
1.73-1.760.23731190.21452655X-RAY DIFFRACTION100
1.76-1.790.25831620.21742581X-RAY DIFFRACTION100
1.79-1.830.22531490.20542621X-RAY DIFFRACTION100
1.83-1.870.26231450.21052605X-RAY DIFFRACTION100
1.87-1.910.21421370.20292656X-RAY DIFFRACTION100
1.91-1.960.22751310.192642X-RAY DIFFRACTION100
1.96-2.020.18871350.16712615X-RAY DIFFRACTION100
2.02-2.080.18571330.16942648X-RAY DIFFRACTION100
2.08-2.140.17261550.16212626X-RAY DIFFRACTION100
2.14-2.220.17871350.15922647X-RAY DIFFRACTION100
2.22-2.310.16181420.1582622X-RAY DIFFRACTION100
2.31-2.410.18291530.16182629X-RAY DIFFRACTION100
2.41-2.540.17551250.15742650X-RAY DIFFRACTION100
2.54-2.70.19331340.16492674X-RAY DIFFRACTION100
2.7-2.910.16581250.16312676X-RAY DIFFRACTION100
2.91-3.20.16711550.17012611X-RAY DIFFRACTION99
3.2-3.660.19131450.1662697X-RAY DIFFRACTION100
3.66-4.610.15481380.1432708X-RAY DIFFRACTION100
4.61-29.250.20191530.17772816X-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)
13.36332.25352.41847.79081.5357.37280.0347-0.5218-0.09990.6755-0.31210.98510.111-0.61270.16960.21260.05020.08170.2561-0.02330.3556-31.76133.993-12.4027
21.6043-0.27440.61621.446-0.38591.8737-0.04420.15550.15970.0777-0.0693-0.1287-0.12960.27710.10660.1576-0.0013-0.00090.18910.00820.1787-17.999914.5198-24.1795
30.72460.1697-0.96090.6979-1.09723.1204-0.0051-0.0735-0.0840.0548-0.12480.00870.12060.12890.1380.27080.03390.04490.1937-0.02040.2452-10.2051-15.9264-2.4069
40.9292-1.15920.92241.4274-1.07920.66820.20220.3078-0.048-0.3426-0.2895-0.06720.30340.23040.09790.34490.10880.02710.3235-0.03650.2776-10.8866-12.752-24.2087
51.4388-0.91520.38892.4321-0.22350.11890.05630.1315-0.1256-0.1374-0.11090.08090.1240.08330.05770.24270.06950.02450.2528-0.03080.1664-12.0066-11.9736-19.1857
60.45213.3046-1.07882.0005-7.92012.59290.412-0.0831.48950.63670.08310.6066-0.6267-0.1413-0.45780.5040.03320.07260.4082-0.07690.5918-24.2022-1.8497-8.1177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 104 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 255 )
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 307 )
4X-RAY DIFFRACTION4chain 'A' and (resid 308 through 349 )
5X-RAY DIFFRACTION5chain 'A' and (resid 350 through 445 )
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 94 )

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