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- PDB-1f3l: CRYSTAL STRUCTURE OF THE CONSERVED CORE OF PROTEIN ARGININE METHY... -

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Basic information

Entry
Database: PDB / ID: 1f3l
TitleCRYSTAL STRUCTURE OF THE CONSERVED CORE OF PROTEIN ARGININE METHYLTRANSFERASE PRMT3
ComponentsPROTEIN ARGININE METHYLTRANSFERASE PRMT3
KeywordsTRANSFERASE / BETA BARREL / ROSSMANN FOLD / ARGININE METHYLTRANSFERASE
Function / homology
Function and homology information


Protein methylation / RMTs methylate histone arginines / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / modified amino acid binding / peptidyl-arginine methylation / protein-arginine omega-N asymmetric methyltransferase activity / protein methylation / protein-arginine N-methyltransferase activity / dendritic spine morphogenesis / S-adenosylmethionine-dependent methyltransferase activity ...Protein methylation / RMTs methylate histone arginines / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / modified amino acid binding / peptidyl-arginine methylation / protein-arginine omega-N asymmetric methyltransferase activity / protein methylation / protein-arginine N-methyltransferase activity / dendritic spine morphogenesis / S-adenosylmethionine-dependent methyltransferase activity / negative regulation of protein ubiquitination / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / ribosome binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / 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 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å
AuthorsZhang, X. / Zhou, L. / Cheng, X.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of the conserved core of protein arginine methyltransferase PRMT3.
Authors: Zhang, X. / Zhou, L. / Cheng, X.
History
DepositionJun 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 METHYLTRANSFERASE PRMT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5932
Polymers36,2091
Non-polymers3841
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN ARGININE METHYLTRANSFERASE PRMT3
hetero molecules

A: PROTEIN ARGININE METHYLTRANSFERASE PRMT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1864
Polymers72,4172
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+5/21
Buried area3280 Å2
ΔGint-30 kcal/mol
Surface area26170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.910, 70.910, 177.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN ARGININE METHYLTRANSFERASE PRMT3


Mass: 36208.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: O70467
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG4000, AMMONIUM ACETATE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMMes11
216.5-18 %PEG400011
30.2 Mammonium acetate11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
SYNCHROTRONNSLS X12C10.930.93
SYNCHROTRONNSLS X26C21.11.1
ROTATING ANODEOTHER31.54181.5418
Detector
TypeIDDetectorDate
BRANDEIS - B21CCDMay 1, 1999
ADSC QUANTUM 42CCDMay 1, 1999
RIGAKU RAXIS IV3IMAGE PLATEApr 28, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.931
21.11
31.54181
ReflectionResolution: 2→30 Å / Biso Wilson estimate: 5 Å2
Reflection
*PLUS
Highest resolution: 2.03 Å / Num. obs: 27345 / % possible obs: 90.9 % / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 56.9 % / Num. unique obs: 1659 / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.03→29.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 252423.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2339 9 %RANDOM
Rwork0.209 ---
obs0.209 26048 86.6 %-
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.03→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 26 149 2671
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.261.5
X-RAY DIFFRACTIONx_mcangle_it2.032
X-RAY DIFFRACTIONx_scbond_it2.232
X-RAY DIFFRACTIONx_scangle_it3.362.5
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 214 8.7 %
Rwork0.274 2259 -
obs--50.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3CN
X-RAY DIFFRACTION4WATER_REP.PARAM
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71

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