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- PDB-7uq3: JmjC domain-containing protein 5 (JMJD5) in complex with Mn and (... -

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Basic information

Entry
Database: PDB / ID: 7uq3
TitleJmjC domain-containing protein 5 (JMJD5) in complex with Mn and (S)-2-(1-hydroxy-2,5-dioxopyrrolidin-3-yl)acetic acid
ComponentsBifunctional peptidase and arginyl-hydroxylase JMJD5
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / JMJC / JMJC DOMAIN / Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Arginyl C-3 Hydroxylase / JMJD5 / KDM8 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSLATION / DSBH / FACIAL TRIAD / CYTOPLASM / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / BETA-HYDROXYLATION / HYDROXYLATION / ARGININE HYDROXYLATION / RCC1 domain-containing protein 1 / RCCD1 / Regulator of chromosome condensation / 40S ribosomal protein S6 / RPS6 / RIBOSOME BIOGENESIS / TRANSCRIPTION / EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / CANCER / POLYMORPHISM
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 / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile.
Similarity search - Domain/homology
: / Chem-O2U / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsChowdhury, R. / Islam, M.S. / Schofield, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Sci Rep / Year: 2022
Title: Structural analysis of the 2-oxoglutarate binding site of the circadian rhythm linked oxygenase JMJD5.
Authors: Islam, M.S. / Markoulides, M. / Chowdhury, R. / Schofield, C.J.
History
DepositionApr 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional peptidase and arginyl-hydroxylase JMJD5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1465
Polymers29,7341
Non-polymers4124
Water5,224290
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)49.479, 64.690, 78.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bifunctional peptidase and arginyl-hydroxylase JMJD5 / JmjC domain-containing protein 5 / Jumonji C domain-containing protein 5 / L-arginine (3R)-hydroxylase KDM8


Mass: 29733.547 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(DE3) (bacteria)
References: UniProt: Q8N371, [protein]-arginine 3-hydroxylase, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-O2U / [(3S)-1-hydroxy-2,5-dioxopyrrolidin-3-yl]acetic acid


Mass: 173.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sample: 22 mg/mL JMJD5, 1.5 mM MnCl2, 5 mM compound (IS-52); Reservoir: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2; Cryo-protection: 25% (v/v) glycerol; Method: 300 nL sitting ...Details: Sample: 22 mg/mL JMJD5, 1.5 mM MnCl2, 5 mM compound (IS-52); Reservoir: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2; Cryo-protection: 25% (v/v) glycerol; Method: 300 nL sitting drops (sample:well, 2:1 ratio)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.49→78.23 Å / Num. obs: 41815 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.04 / Rrim(I) all: 0.107 / Rsym value: 0.099 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.49-1.52720580.7850.330.8880.823100
8.16-78.236.53160.9910.0410.1120.10499.5

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GJZ

4gjz


Resolution: 1.49→49.853 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1349 2107 5.05 %
Rwork0.1339 39639 -
obs0.1347 41747 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.15 Å2 / Biso mean: 21.1625 Å2 / Biso min: 6.89 Å2
Refinement stepCycle: final / Resolution: 1.49→49.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 46 291 2193
Biso mean--31.21 35.85 -
Num. residues----228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.49-1.54330.18081920.17843959
1.5433-1.60510.14922200.14763854
1.6051-1.67810.16061940.1353913
1.6781-1.76660.1391920.12033949
1.7666-1.87730.09782000.11533916
1.8773-2.02220.12012350.1123924
2.0222-2.22570.10892270.11383941
2.2257-2.54780.10951930.11643993
2.5478-3.20990.13272290.13184007
3.2099-49.8530.15852250.15494183

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