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- PDB-4m36: Crystal structure of Trypanosoma brucei protein arginine methyltr... -

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Basic information

Entry
Database: PDB / ID: 4m36
TitleCrystal structure of Trypanosoma brucei protein arginine methyltransferase 7
ComponentsProtein arginine N-methyltransferase 7
KeywordsTRANSFERASE / Methyltransferase
Function / homology
Function and homology information


arginine N-methyltransferase activity / : / peptidyl-arginine N-methylation / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine methylation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / protein-containing complex / identical protein binding / 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. / 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
Protein arginine N-methyltransferase 7
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.042 Å
AuthorsWang, C. / Zhu, Y. / Shi, Y.
CitationJournal: Structure / Year: 2014
Title: Structural determinants for the strict monomethylation activity by trypanosoma brucei protein arginine methyltransferase 7.
Authors: Wang, C. / Zhu, Y. / Caceres, T.B. / Liu, L. / Peng, J. / Wang, J. / Chen, J. / Chen, X. / Zhang, Z. / Zuo, X. / Gong, Q. / Teng, M. / Hevel, J.M. / Wu, J. / Shi, Y.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 7


Theoretical massNumber of molelcules
Total (without water)38,9851
Polymers38,9851
Non-polymers00
Water3,639202
1
A: Protein arginine N-methyltransferase 7

A: Protein arginine N-methyltransferase 7


Theoretical massNumber of molelcules
Total (without water)77,9712
Polymers77,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6810 Å2
ΔGint-41 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.621, 40.857, 90.538
Angle α, β, γ (deg.)90.00, 131.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein arginine N-methyltransferase 7 / TbPRMT7


Mass: 38985.469 Da / Num. of mol.: 1 / Fragment: UNP residues 36-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: PRMT7, Tb927.7.5490 / Production host: Escherichia coli (E. coli)
References: UniProt: Q582G4, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES , 20% PEG 1000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9791 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: NiFILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 23151

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.042→49.226 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8679 / SU ML: 0.19 / σ(F): 1.36 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2057 1184 5.11 %
Rwork0.1639 --
obs0.1661 23151 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.48 Å2 / Biso mean: 10.7354 Å2 / Biso min: 2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.042→49.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 0 202 2857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072721
X-RAY DIFFRACTIONf_angle_d1.1113696
X-RAY DIFFRACTIONf_dihedral_angle_d12.7671004
X-RAY DIFFRACTIONf_chiral_restr0.074415
X-RAY DIFFRACTIONf_plane_restr0.005483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.042-2.13490.21821390.13992690282999
2.1349-2.24750.24641390.157527222861100
2.2475-2.38830.25581550.162827222877100
2.3883-2.57270.23681190.170327582877100
2.5727-2.83160.2261550.178627442899100
2.8316-3.24120.22921460.176727432889100
3.2412-4.08330.16341400.159327872927100
4.0833-49.24040.17491910.159828012992100

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