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- PDB-5g02: Crystal Structure of zebrafish Protein Arginine Methyltransferase... -

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Basic information

Entry
Database: PDB / ID: 5g02
TitleCrystal Structure of zebrafish Protein Arginine Methyltransferase 2 with SFG
ComponentsPROTEIN ARGININE METHYLTRANSFERASE 2
KeywordsTRANSFERASE / S-ADENOSYL-L-METHIONINE / S-ADENOSYL-L- HOMOCYSTEINE
Function / homology
Function and homology information


peptidyl-arginine methylation / protein-arginine N-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / identical protein binding / 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. / SH3 domain / Vaccinia Virus protein VP39 / Distorted Sandwich / Src homology 3 domains ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / 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
: / SINEFUNGIN / Protein arginine methyltransferase 2
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.451 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
DepositionMar 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Mar 1, 2017Group: Database references
Revision 1.4Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN ARGININE METHYLTRANSFERASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8287
Polymers38,9251
Non-polymers9036
Water28816
1
A: PROTEIN ARGININE METHYLTRANSFERASE 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)238,97042
Polymers233,5526
Non-polymers5,41836
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area25260 Å2
ΔGint-23.6 kcal/mol
Surface area74340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.994, 147.994, 127.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1411-

LI

21A-2001-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN ARGININE METHYLTRANSFERASE 2 / PROTEIN ARGININE N-METHYLTRANSFERASE 2


Mass: 38925.328 Da / Num. of mol.: 1 / Fragment: METHYLATION MODULE, UNP RESIDUES 68-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Description: BIOSCIENCE IRAK293-C16 / Plasmid: PDEST20 / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: A1L1Q4, EC: 2.1.1.125

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Non-polymers , 5 types, 22 molecules

#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCRYSTALLIZED PRMT2 SEQUENCE STARTS AT T68.

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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: 3.46 Å3/Da / Density % sol: 64.5 % / Description: STARTING MODEL GENERATED BY BALBES
Crystal growpH: 6 / Details: 10% PEG20000, 100MM LICL,100MM MES PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.45→45.3 Å / Num. obs: 19847 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.8
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.451→45.293 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 1025 5.2 %
Rwork0.1902 --
obs0.1921 19829 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.5 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 76 Å2
Refinement stepCycle: LAST / Resolution: 2.451→45.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2701 0 60 16 2777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072828
X-RAY DIFFRACTIONf_angle_d0.9363838
X-RAY DIFFRACTIONf_dihedral_angle_d16.9691652
X-RAY DIFFRACTIONf_chiral_restr0.051424
X-RAY DIFFRACTIONf_plane_restr0.004480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4507-2.57990.36841500.30642645X-RAY DIFFRACTION99
2.5799-2.74150.30491560.2732636X-RAY DIFFRACTION100
2.7415-2.95310.30491490.27432660X-RAY DIFFRACTION100
2.9531-3.25020.30881610.26392658X-RAY DIFFRACTION100
3.2502-3.72030.23931470.21612680X-RAY DIFFRACTION100
3.7203-4.68650.19571400.15632713X-RAY DIFFRACTION100
4.6865-45.30030.18221220.15022812X-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)
12.581-0.6020.61671.4847-0.52864.92340.0156-0.0756-0.0502-0.0037-0.1398-0.1798-1.01880.25730.0260.7898-0.0793-0.05880.3535-0.01420.51274.386524.049248.0946
22.3664-0.18590.12451.4608-0.18433.940.1040.24660.042-0.2366-0.06270.2817-0.9649-0.23-0.01890.77330.0045-0.05290.3314-0.01020.5112-1.219123.722637.185
30.98940.0181.23950.3546-0.1294.6535-0.130.15590.16570.1248-0.1343-0.2727-0.91171.40090.07870.6753-0.40040.02220.9977-0.02190.625229.186417.888862.5828
42.3214-0.3411.10121.52630.3693.1889-0.00580.28510.3918-0.2251-0.1605-0.2586-1.24291.29950.1130.8393-0.46610.07710.90680.04460.560922.891723.54740.7949
52.547-0.46710.60491.2915-0.12993.4029-0.10770.25460.4084-0.21030.2146-0.6025-0.59292.05170.01340.622-0.28760.05881.2643-0.02540.618332.954715.421748.7409
63.13410.3431.14882.46080.12443.8092-0.0512-0.182-0.3215-0.1251-0.0357-0.4237-0.0561.4468-0.09780.4362-0.09490.03480.8277-0.00640.543426.34337.943948.1685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 72 THROUGH 109 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 110 THROUGH 221 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 222 THROUGH 273 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 274 THROUGH 350 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 351 THROUGH 375 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 376 THROUGH 408 )

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