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- PDB-6pdm: Crystal structure of Human Protein Arginine Methyltransferase 9 (... -

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Basic information

Entry
Database: PDB / ID: 6pdm
TitleCrystal structure of Human Protein Arginine Methyltransferase 9 (PRMT9)
ComponentsProtein arginine N-methyltransferase 9
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity ...type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / histone H2AQ104 methyltransferase activity / histone methyltransferase activity / mRNA processing / methylation / chromatin remodeling / regulation of DNA-templated transcription / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L11 methyltransferase (PrmA) / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protein arginine N-methyltransferase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHalabelian, L. / Tempel, W. / Zeng, H. / Li, Y. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of Human Protein Arginine Methyltransferase 9 (PRMT9)
Authors: Halabelian, L. / Tempel, W. / Zeng, H. / Li, Y. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionJun 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 9


Theoretical massNumber of molelcules
Total (without water)80,48614
Polymers80,4861
Non-polymers013
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.812, 83.802, 65.711
Angle α, β, γ (deg.)90.000, 98.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein arginine N-methyltransferase 9 / Protein arginine N-methyltransferase 10


Mass: 80486.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT9, PRMT10 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6P2P2, type II protein arginine methyltransferase
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2M ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→65.05 Å / Num. obs: 27005 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 69.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 11 / Num. measured all: 92810
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.493.61.208972827040.4680.7391.4190.994.7
8.97-65.053.40.02218465510.9990.0140.02645.599.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHENIX.MR_ROSETTA with PDB entry 4C4A

4c4a


Resolution: 2.45→65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.37 / SU Rfree Blow DPI: 0.256 / Details: geometry restrained to PHENIX.ROSETTA_REFINE model
RfactorNum. reflection% reflection
Rfree0.26 1310 5.15 %
Rwork0.216 --
obs0.219 25460 99 %
Displacement parametersBiso max: 133.49 Å2 / Biso mean: 66.62 Å2 / Biso min: 42.41 Å2
Baniso -1Baniso -2Baniso -3
1--3.478 Å20 Å213.2393 Å2
2---2.1813 Å20 Å2
3---5.6593 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.45→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 13 0 4482
Biso mean--58.93 --
Num. residues----614
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1849SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1342HARMONIC5
X-RAY DIFFRACTIONt_it8784HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion652SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9510SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8784HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15886HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion12.63
LS refinement shellResolution: 2.45→2.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.234 148 5.15 %
Rwork0.206 2728 -
all0.208 2876 -
obs--99.34 %

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