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- PDB-7dyu: Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridi... -

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Basic information

Entry
Database: PDB / ID: 7dyu
TitleHuman JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridine-2,4-dicarboxylic acid.
ComponentsBifunctional peptidase and arginyl-hydroxylase JMJD5
KeywordsOXIDOREDUCTASE / JmjC domain-containing protein 5 / JMJD5 / dioxygenase
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-HR9 / : / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
CitationJournal: J.Med.Chem. / Year: 2023
Title: 5-Substituted Pyridine-2,4-dicarboxylate Derivatives Have Potential for Selective Inhibition of Human Jumonji-C Domain-Containing Protein 5.
Authors: Brewitz, L. / Nakashima, Y. / Piasecka, S.K. / Salah, E. / Fletcher, S.C. / Tumber, A. / Corner, T.P. / Kennedy, T.J. / Fiorini, G. / Thalhammer, A. / Christensen, K.E. / Coleman, M.L. / Schofield, C.J.
History
DepositionJan 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Dec 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,8755
Polymers27,2621
Non-polymers6144
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-6 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.372, 64.564, 78.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 27261.873 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(DE3) (bacteria)
References: UniProt: Q8N371, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen ...References: UniProt: Q8N371, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-HR9 / 5-(4-phenylbutylamino)pyridine-2,4-dicarboxylic acid


Mass: 314.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.72→49.86 Å / Num. obs: 38768 / % possible obs: 94.2 % / Redundancy: 12.4 % / Biso Wilson estimate: 22.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.155 / Net I/σ(I): 11.9
Reflection shellResolution: 1.72→1.85 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.805 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1040 / CC1/2: 0.351 / % possible all: 58.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F4P

6f4p


Resolution: 1.72→49.86 Å / SU ML: 0.1264 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 22.1821
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1946 1849 4.77 %
Rwork0.1595 36919 -
obs0.1612 38768 75.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.67 Å2
Refinement stepCycle: LAST / Resolution: 1.72→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1859 0 31 182 2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01722072
X-RAY DIFFRACTIONf_angle_d1.27092844
X-RAY DIFFRACTIONf_chiral_restr0.0866291
X-RAY DIFFRACTIONf_plane_restr0.0104374
X-RAY DIFFRACTIONf_dihedral_angle_d18.2955765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.770.4085120.3717220X-RAY DIFFRACTION5.79
1.77-1.820.3733390.3274802X-RAY DIFFRACTION21.26
1.82-1.880.2977940.28671333X-RAY DIFFRACTION36.66
1.88-1.940.3819990.26482227X-RAY DIFFRACTION58.49
1.94-2.020.23711240.22772803X-RAY DIFFRACTION73.82
2.02-2.110.23661680.20663222X-RAY DIFFRACTION85.71
2.11-2.230.24681660.19543704X-RAY DIFFRACTION97.68
2.23-2.370.21251790.16863784X-RAY DIFFRACTION100
2.37-2.550.21482150.15513727X-RAY DIFFRACTION100
2.55-2.80.18021820.13973798X-RAY DIFFRACTION100
2.8-3.210.1741850.1313774X-RAY DIFFRACTION99.97
3.21-4.040.15282110.12253755X-RAY DIFFRACTION100
4.04-49.860.17751750.1593770X-RAY DIFFRACTION99.92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.03186466289-0.00729924901264-0.1801224915361.62272469830.99836158352.72182521777-0.08385798468590.06560881652490.2820224036970.1660884728420.2668886946720.359936633727-0.252225869835-0.51551092273-0.05785527291560.1369434433810.08765012388750.02861433803620.2137599297960.05833419746050.214516317887-25.642853049122.4473516056-21.2721031016
21.74584318042-1.360037769940.5803719512851.4552189799-0.5214268397352.01866987148-0.396173113493-0.45311257171-0.01294100691960.691436814390.4189304885270.0978241327864-0.311632298263-0.156823630472-0.01084709960890.3162676398150.07048585591770.04029896640650.242047233107-0.01680959134430.162704794517-11.372492228313.8386221259-5.90733974654
36.374705357171.97889726174-2.269647270787.80061527491-0.7814952491646.8927508058-0.05287232137130.495735643461-0.3225067386-0.224618712832-0.0791542061087-0.3219780294040.2247706596320.1699122319810.08898532237510.1092405555150.05548394268510.03193642142280.155697551438-5.74437542534E-50.1728652846093.936057575732.928522681-15.0394594683
42.8216596058-0.7163094255891.083142132491.89941648566-0.3250633457221.44218130689-0.0696832675137-0.144169198367-0.347802366720.1681123490760.07710797928850.05030787801030.110730543899-0.0680451967796-0.0295043309110.179237642573-0.008334168083380.04450748451930.1326655816450.02640810996740.174553923758-8.640511510597.24069941383-13.008244049
52.557822834370.2996101417870.03904127394343.078013877070.2252762772232.82125674219-0.0899831135315-0.0470735531486-0.4012912743420.097626783290.1295700154570.6103273358740.557180721108-0.70735989666-0.01751482145670.164271398404-0.0565030540050.05234714305390.1073606206010.004314234458280.246658208709-17.39742459994.77736220633-18.4272975791
62.003420709410.233574984774-0.8989773469031.79505104141-0.8013389959912.155404638120.02965439071920.21323597909-0.0407115822543-0.05738513326490.0345865524914-0.0363825213368-0.0266027366246-0.048272963089-0.0855379344470.07375189455710.0195608417987-0.001014793801690.0609257404554-0.01753608772180.08257599584-8.8736519452517.3505849052-28.150989984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 182 through 205 )
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 230 )
3X-RAY DIFFRACTION3chain 'A' and (resid 231 through 262 )
4X-RAY DIFFRACTION4chain 'A' and (resid 263 through 297 )
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 312 )
6X-RAY DIFFRACTION6chain 'A' and (resid 313 through 416 )

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