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- PDB-5hzm: Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae) -

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Basic information

Entry
Database: PDB / ID: 5hzm
TitleHuman HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae)
ComponentsProtein arginine N-methyltransferase 6
KeywordsTRANSFERASE / HRMT1L6 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone H3 methyltransferase activity / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / protein modification process / base-excision repair / RMTs methylate histone arginines / cellular senescence / histone binding / methylation / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / 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. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / Methyltransferase domain / 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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsDONG, A. / ZENG, H. / WALKER, J.R. / Seitova, A. / Hutchinson, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / MIN, J. ...DONG, A. / ZENG, H. / WALKER, J.R. / Seitova, A. / Hutchinson, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / MIN, J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem. J. / Year: 2016
Title: Structural basis of arginine asymmetrical dimethylation by PRMT6.
Authors: Wu, H. / Zheng, W. / Eram, M.S. / Vhuiyan, M. / Dong, A. / Zeng, H. / He, H. / Brown, P. / Frankel, A. / Vedadi, M. / Luo, M. / Min, J.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,45912
Polymers42,0751
Non-polymers38411
Water3,297183
1
A: Protein arginine N-methyltransferase 6
hetero molecules

A: Protein arginine N-methyltransferase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,91824
Polymers84,1492
Non-polymers76922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Buried area4580 Å2
ΔGint-37 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.190, 94.190, 109.609
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Protein arginine N-methyltransferase 6 / Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N- ...Heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 6 / Histone-arginine N-methyltransferase PRMT6


Mass: 42074.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT6, HRMT1L6 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q96LA8, type I protein arginine methyltransferase
#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: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 10% PEG 8000, 0.1 M Tris-HCL pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.25496 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25496 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 31311 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Χ2: 1.167 / Net I/av σ(I): 36.633 / Net I/σ(I): 9.7 / Num. measured all: 232791
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.02-2.057.40.9861100
2.05-2.097.40.7961100
2.09-2.137.40.6481100
2.13-2.187.40.5441100
2.18-2.227.40.4411100
2.22-2.277.40.3711100
2.27-2.337.50.321100
2.33-2.397.50.2721100
2.39-2.477.50.2211100
2.47-2.547.50.1821100
2.54-2.647.50.1521100
2.64-2.747.50.1171100
2.74-2.877.50.0981100
2.87-3.027.50.0831100
3.02-3.217.50.0721100
3.21-3.457.50.0611100
3.45-3.87.40.0491100
3.8-4.357.30.0361100
4.35-5.487.40.031100
5.48-507.40.028199.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-3000phasing
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HC4

4hc4


Resolution: 2.02→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.683 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 991 3.2 %RANDOM
Rwork0.1752 ---
obs0.1762 30302 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.69 Å2 / Biso mean: 40.917 Å2 / Biso min: 19.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 36 188 2781
Biso mean--33.53 48.65 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192739
X-RAY DIFFRACTIONr_bond_other_d0.0020.022587
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9633733
X-RAY DIFFRACTIONr_angle_other_deg0.93135941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0565349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00322.742124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99115453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0631525
X-RAY DIFFRACTIONr_chiral_restr0.0840.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213126
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02659
X-RAY DIFFRACTIONr_mcbond_it2.5153.8661343
X-RAY DIFFRACTIONr_mcbond_other2.5153.8661342
X-RAY DIFFRACTIONr_mcangle_it3.555.781685
LS refinement shellResolution: 2.02→2.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 61 -
Rwork0.269 2232 -
all-2293 -
obs--99.57 %

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