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- PDB-3r0q: A Uniquely Open Conformation Revealed in the Crystal Structure of... -

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Basic information

Entry
Database: PDB / ID: 3r0q
TitleA Uniquely Open Conformation Revealed in the Crystal Structure of Arabidopsis Thaliana Protein Arginine Methyltransferase 10
ComponentsProbable protein arginine N-methyltransferase 4.2Probability
KeywordsTRANSFERASE / Arginine methyltransferase / Methylation
Function / homology
Function and homology information


: / peptidyl-arginine methylation, to asymmetrical-dimethyl arginine / vegetative to reproductive phase transition of meristem / protein-arginine omega-N monomethyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / cytosol
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. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich ...Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / 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 PRMT10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsCheng, Y. / Redinbo, M.R.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structure of the plant epigenetic protein arginine methyltransferase 10.
Authors: Cheng, Y. / Frazier, M. / Lu, F. / Cao, X. / Redinbo, M.R.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
C: Probable protein arginine N-methyltransferase 4.2
G: Probable protein arginine N-methyltransferase 4.2
A: Probable protein arginine N-methyltransferase 4.2
E: Probable protein arginine N-methyltransferase 4.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,2568
Polymers169,7194
Non-polymers1,5384
Water3,027168
1
C: Probable protein arginine N-methyltransferase 4.2
A: Probable protein arginine N-methyltransferase 4.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6284
Polymers84,8592
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-27 kcal/mol
Surface area28270 Å2
MethodPISA
2
G: Probable protein arginine N-methyltransferase 4.2
E: Probable protein arginine N-methyltransferase 4.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6284
Polymers84,8592
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-27 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.552, 86.691, 114.735
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable protein arginine N-methyltransferase 4.2 / Probability


Mass: 42429.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRMT4.2, At1g04870, F13M7.14, F13M7_12 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9MAT5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1M Tris-HCl, 2.3M Na2HPO4, 0.1M arginine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 10, 2009
RadiationMonochromator: VariMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.61→32.97 Å / Num. all: 48404 / Num. obs: 46744 / % possible obs: 96.57 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.12
Reflection shellResolution: 2.61→2.67 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.58 / % possible all: 91

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→32.97 Å / σ(F): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 2037 4.36 %Random
Rwork0.1821 ---
all0.1846 48404 --
obs0.1846 46744 96.57 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.883 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7015 Å20 Å2-0.1818 Å2
2--8.0968 Å20 Å2
3----3.3953 Å2
Refinement stepCycle: LAST / Resolution: 2.61→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10753 0 104 168 11025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711119
X-RAY DIFFRACTIONf_angle_d1.16615135
X-RAY DIFFRACTIONf_dihedral_angle_d16.2283873
X-RAY DIFFRACTIONf_chiral_restr0.0751681
X-RAY DIFFRACTIONf_plane_restr0.0041946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.67460.41021330.34953093X-RAY DIFFRACTION91
2.6746-2.74680.40351380.29873237X-RAY DIFFRACTION94
2.7468-2.82760.3071500.27223216X-RAY DIFFRACTION94
2.8276-2.91870.32231370.25343266X-RAY DIFFRACTION95
2.9187-3.02290.29311490.2383250X-RAY DIFFRACTION95
3.0229-3.14370.28741580.20783245X-RAY DIFFRACTION95
3.1437-3.28650.24981370.19643267X-RAY DIFFRACTION95
3.2865-3.45950.22661440.17983217X-RAY DIFFRACTION94
3.4595-3.67570.2061300.16863256X-RAY DIFFRACTION94
3.6757-3.95860.18911500.14723169X-RAY DIFFRACTION92
3.9586-4.35530.13511450.13653194X-RAY DIFFRACTION93
4.3553-4.98180.19021470.12623154X-RAY DIFFRACTION91
4.9818-6.26240.19561410.1633102X-RAY DIFFRACTION89
6.2624-26.2360.20151330.17033037X-RAY DIFFRACTION86

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