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- PDB-6f4m: Human JMJD5 in its apo form. -

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Basic information

Entry
Database: PDB / ID: 6f4m
TitleHuman JMJD5 in its apo form.
ComponentsJmjC domain-containing protein 5
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 / 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
Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.705 Å
AuthorsChowdhury, R. / Islam, M.S. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2018
Title: JMJD5 is a human arginyl C-3 hydroxylase.
Authors: Wilkins, S.E. / Islam, S. / Gannon, J.M. / Markolovic, S. / Hopkinson, R.J. / Ge, W. / Schofield, C.J. / Chowdhury, R.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: JmjC domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)27,1341
Polymers27,1341
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.033, 66.438, 70.076
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 JmjC domain-containing protein 5 / LYSINE-SPECIFIC DEMETHYLASE 8 / JUMONJI DOMAIN-CONTAINING PROTEIN 5 /


Mass: 27133.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (RESIDUES 183-416) / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM8, JMJD5 / Plasmid: PNIC28 BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8N371, [50S ribosomal protein L16]-arginine 3-hydroxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 22.5 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2016 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→48.21 Å / Num. obs: 25416 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.04 / Net I/σ(I): 21.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 13 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2481 / CC1/2: 0.52 / Rpim(I) all: 0.791 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000706Edata reduction
HKL-2000706Edata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GJZ

4gjz


Resolution: 1.705→48.21 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.46
Details: REFINEMENT TARGET: ML and BULK SOLVENT MODELLING METHOD USED: FLAT MODEL
RfactorNum. reflection% reflection
Rfree0.1865 1246 4.91 %
Rwork0.1696 --
obs0.1705 25366 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 56.9 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.53 Å20 Å2
3---0.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.2 Å
Refinement stepCycle: LAST / Resolution: 1.705→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 0 207 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052043
X-RAY DIFFRACTIONf_angle_d0.7642802
X-RAY DIFFRACTIONf_dihedral_angle_d16.6711211
X-RAY DIFFRACTIONf_chiral_restr0.053294
X-RAY DIFFRACTIONf_plane_restr0.005370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7055-1.77380.36791070.29672476X-RAY DIFFRACTION93
1.7738-1.85450.27551380.24642657X-RAY DIFFRACTION100
1.8545-1.95230.2441560.21392637X-RAY DIFFRACTION100
1.9523-2.07460.19821520.17242656X-RAY DIFFRACTION100
2.0746-2.23480.19631420.16642681X-RAY DIFFRACTION100
2.2348-2.45960.18851430.16592694X-RAY DIFFRACTION100
2.4596-2.81550.19051030.16942731X-RAY DIFFRACTION100
2.8155-3.54710.18521460.15862733X-RAY DIFFRACTION100
3.5471-48.23280.15751590.15412855X-RAY DIFFRACTION100
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)
11.60670.10620.12871.51581.03861.29180.00160.1113-0.1530.05180.10810.32810.4903-0.61880.01480.1767-0.06140.01570.27190.01830.2439-25.48136.5216-15.0789
20.66610.07760.49890.4309-0.44490.5585-0.0454-0.09390.0169-0.24490.07750.00370.1584-0.07540.00010.2498-0.0256-0.00620.2008-0.00160.1884-10.459717.479-33.0097
31.73490.6203-0.94752.13650.73281.08060.1001-0.3804-0.07430.4740.0115-0.0558-0.07720.09510.00010.2268-0.0306-0.04510.2359-0.00880.21984.20124.398-16.2739
41.50491.28080.58542.1814-0.78891.64760.0318-0.62730.26630.3948-0.095-0.3257-0.08190.26380.00370.1835-0.0139-0.02180.2635-0.00380.23694.23321.6692-22.1603
51.17680.30040.60430.7087-0.53221.24890.1966-0.01030.71180.33590.01870.2228-0.5712-0.32170.00360.28070.00820.04490.2515-0.02510.3254-18.638424.0581-23.1061
61.8258-0.7489-1.26990.21310.42780.9224-0.3315-0.31370.08570.65380.2424-0.0341-0.040.3103-0.00340.26180.01910.06940.1834-0.02980.3258-9.422821.0854-20.7106
70.45820.03950.54230.1271-0.12460.81870.0646-0.07370.15390.1417-0.183-0.1698-0.21560.057-0.00010.2002-0.01880.00770.2303-0.01020.2029-6.365714.7654-11.0434
81.12820.23470.13030.4906-0.23760.21430.04060.041-0.03480.0073-0.1013-0.02860.0922-0.028800.1743-0.0172-0.00190.14230.01840.1513-11.17689.8522-16.4075
91.5371-0.71661.0361.10750.27042.103-0.0147-0.31640.03490.0339-0.0077-0.3155-0.40090.0294-00.3241-0.0178-0.01840.214-0.04350.1756-6.386813.89110.0367
100.9084-0.90780.23621.30460.4040.70980.2682-0.1961-0.4370.0997-0.0313-0.25470.2543-0.04470.00040.2659-0.0452-0.06610.22830.06740.2618-2.2852.9660.9438
111.2489-0.7270.93840.9361-0.97630.9475-0.087-0.07390.0514-0.0165-0.00790.02140.118-0.1562-00.1564-0.02340.00760.1603-0.01080.1564-15.00958.9942-13.2691
120.64880.4737-0.02150.5155-0.63791.26640.0521-0.02740.17890.051-0.1052-0.1318-0.1683-0.0009-00.1881-0.00880.01350.1395-0.00180.1749-9.757514.3601-17.9809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 182:211)
2X-RAY DIFFRACTION2(chain A and resid 212:230)
3X-RAY DIFFRACTION3(chain A and resid 231:254)
4X-RAY DIFFRACTION4(chain A and resid 255:277)
5X-RAY DIFFRACTION5(chain A and resid 278:305)
6X-RAY DIFFRACTION6(chain A and resid 306:312)
7X-RAY DIFFRACTION7(chain A and resid 313:325)
8X-RAY DIFFRACTION8(chain A and resid 326:341)
9X-RAY DIFFRACTION9(chain A and resid 342:365)
10X-RAY DIFFRACTION10(chain A and resid 366:381)
11X-RAY DIFFRACTION11(chain A and resid 382:399)
12X-RAY DIFFRACTION12(chain A and resid 400:416)

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