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- PDB-4m37: Crystal structure of Trypanosoma brucei protein arginine methyltr... -

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Basic information

Entry
Database: PDB / ID: 4m37
TitleCrystal structure of Trypanosoma brucei protein arginine methyltransferase 7 complex with AdoHcy
ComponentsProtein arginine N-methyltransferase 7
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


arginine N-methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine N-methylation / peptidyl-arginine methylation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / chromatin remodeling / regulation of DNA-templated transcription ...arginine N-methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine N-methylation / peptidyl-arginine methylation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / chromatin remodeling / regulation of DNA-templated transcription / 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
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 7
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / Derived calculations / Category: citation / database_2 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3702
Polymers38,9851
Non-polymers3841
Water4,432246
1
A: Protein arginine N-methyltransferase 7
hetero molecules

A: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7404
Polymers77,9712
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7050 Å2
ΔGint-39 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.591, 40.926, 90.838
Angle α, β, γ (deg.)90.00, 131.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-670-

HOH

21A-682-

HOH

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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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 47.44 %
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: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 37966

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→37.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18254 2001 5 %RANDOM
Rwork0.14767 ---
obs0.14943 37966 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20.11 Å2
2---0.75 Å2-0 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 26 246 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192756
X-RAY DIFFRACTIONr_bond_other_d00.022590
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9643744
X-RAY DIFFRACTIONr_angle_other_deg3.62235954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78724.154130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51315461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7631518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213104
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02632
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5261.6721349
X-RAY DIFFRACTIONr_mcbond_other1.4881.671348
X-RAY DIFFRACTIONr_mcangle_it1.9492.511682
X-RAY DIFFRACTIONr_mcangle_other1.9642.5111683
X-RAY DIFFRACTIONr_scbond_it2.2881.9311407
X-RAY DIFFRACTIONr_scbond_other2.2891.9311407
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6472.8112063
X-RAY DIFFRACTIONr_long_range_B_refined2.81614.5253107
X-RAY DIFFRACTIONr_long_range_B_other2.82114.533108
X-RAY DIFFRACTIONr_rigid_bond_restr8.96635346
X-RAY DIFFRACTIONr_sphericity_free22.594583
X-RAY DIFFRACTIONr_sphericity_bonded6.85355445
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 126 -
Rwork0.166 2772 -
obs--98.71 %

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