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- PDB-6ax3: Complex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA) -

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Basic information

Entry
Database: PDB / ID: 6ax3
TitleComplex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA)
ComponentsLysine-specific demethylase 8
KeywordsHYDROLASE / Demethylase / Jumonji / Histone / Endopeptidase / Exopeptidase
Function / homology
Function and homology information


[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
: / KDM8-like, N-terminal ARM repeats / Cupin-like domain 8 / Cupin-like domain / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
N3, N4-DIMETHYLARGININE / 2-OXOGLUTARIC ACID / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLee, S. / Liu, H. / Wang, Y. / Dai, S. / Zhang, G.
CitationJournal: Sci Rep / Year: 2018
Title: Specific Recognition of Arginine Methylated Histone Tails by JMJD5 and JMJD7.
Authors: Liu, H. / Wang, C. / Lee, S. / Ning, F. / Wang, Y. / Zhang, Q. / Chen, Z. / Zang, J. / Nix, J. / Dai, S. / Marrack, P. / Hagman, J. / Kappler, J. / Zhang, G.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Lysine-specific demethylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6894
Polymers27,2751
Non-polymers4143
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.456, 64.706, 77.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Jumonji domain-containing protein 5


Mass: 27274.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM8, JMJD5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-2MR / N3, N4-DIMETHYLARGININE


Type: L-peptide linking / Mass: 202.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N4O2
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH 7.0 8% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→41.64 Å / Num. obs: 11947 / % possible obs: 97 % / Redundancy: 2.6 % / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fbj

5fbj


Resolution: 2.25→41.637 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 1194 9.99 %
Rwork0.206 --
obs0.2114 11946 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→41.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 25 117 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091942
X-RAY DIFFRACTIONf_angle_d1.1822652
X-RAY DIFFRACTIONf_dihedral_angle_d12.1621120
X-RAY DIFFRACTIONf_chiral_restr0.063280
X-RAY DIFFRACTIONf_plane_restr0.007345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.34010.32081170.25071048X-RAY DIFFRACTION87
2.3401-2.44660.32691220.23981112X-RAY DIFFRACTION94
2.4466-2.57560.30551320.23721192X-RAY DIFFRACTION98
2.5756-2.73690.33391350.24141212X-RAY DIFFRACTION99
2.7369-2.94820.27741330.22821205X-RAY DIFFRACTION99
2.9482-3.24470.28561350.21481200X-RAY DIFFRACTION100
3.2447-3.7140.2521360.19621230X-RAY DIFFRACTION100
3.714-4.67830.20431360.16961231X-RAY DIFFRACTION100
4.6783-41.64370.23091480.19621322X-RAY DIFFRACTION100

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