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- PDB-3k2o: Structure of an oxygenase -

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Basic information

Entry
Database: PDB / ID: 3k2o
TitleStructure of an oxygenase
ComponentsBifunctional arginine demethylase and lysyl-hydroxylase JMJD6
KeywordsOXIDOREDUCTASE / Structural Genomics Consortium / SGC / Chromatin regulator / Developmental protein / Differentiation / Dioxygenase / Iron / Metal-binding / mRNA processing / mRNA splicing / Nucleus / Transcription / Transcription regulation
Function / homology
Function and homology information


peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine / histone H3R2 demethylase activity / peptidyl-lysine 5-dioxygenase activity / histone H4R3 demethylase activity / protein demethylase activity / recognition of apoptotic cell / negative regulation of protein homooligomerization / oxidative RNA demethylation / P-TEFb complex binding / oxidative RNA demethylase activity ...peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine / histone H3R2 demethylase activity / peptidyl-lysine 5-dioxygenase activity / histone H4R3 demethylase activity / protein demethylase activity / recognition of apoptotic cell / negative regulation of protein homooligomerization / oxidative RNA demethylation / P-TEFb complex binding / oxidative RNA demethylase activity / 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 / macrophage activation / non-membrane-bounded organelle assembly / transcription regulator activator activity / regulation of mRNA splicing, via spliceosome / sprouting angiogenesis / Protein hydroxylation / histone demethylase activity / erythrocyte development / phagocytosis / RNA splicing / lung development / kidney development / HDMs demethylate histones / protein homooligomerization / mRNA processing / retina development in camera-type eye / signaling receptor activity / heart development / T cell differentiation in thymus / cell surface receptor signaling pathway / single-stranded RNA binding / chromatin remodeling / ribonucleoprotein complex / iron ion binding / positive regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Monooxygenase - #270 / : / Monooxygenase / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Up-down Bundle ...Monooxygenase - #270 / : / Monooxygenase / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / PHOSPHATE ION / Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKrojer, T. / McDonough, M.A. / Clifton, I.J. / Mantri, M. / Ng, S.S. / Pike, A.C.W. / Butler, D.S. / Webby, C.J. / Kochan, G. / Bhatia, C. ...Krojer, T. / McDonough, M.A. / Clifton, I.J. / Mantri, M. / Ng, S.S. / Pike, A.C.W. / Butler, D.S. / Webby, C.J. / Kochan, G. / Bhatia, C. / Bray, J.E. / Chaikuad, A. / Gileadi, O. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Schofield, C.J. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6.
Authors: Mantri, M. / Krojer, T. / Bagg, E.A. / Webby, C.A. / Butler, D.S. / Kochan, G. / Kavanagh, K.L. / Oppermann, U. / McDonough, M.A. / Schofield, C.J.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
B: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,66618
Polymers79,7952
Non-polymers87116
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-17 kcal/mol
Surface area33830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.440, 102.030, 98.218
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 / Histone arginine demethylase JMJD6 / Peptide-lysine 5-dioxygenase JMJD6 / Lysyl-hydroxylase JMJD6 / ...Histone arginine demethylase JMJD6 / Peptide-lysine 5-dioxygenase JMJD6 / Lysyl-hydroxylase JMJD6 / JmjC domain-containing protein 6 / Jumonji domain-containing protein 6 / Phosphatidylserine receptor / Protein PTDSR


Mass: 39897.441 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD6, KIAA0585, PTDSR / Production host: Escherichia coli (E. coli)
References: UniProt: Q6NYC1, 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

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Non-polymers , 7 types, 689 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.8M NaH2PO4, 0.8M KH2PO4, 0.1M NaHEPES 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→148 Å / Num. obs: 95190 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 9.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.7 / Num. unique all: 13969 / Rsym value: 0.437 / % possible all: 98.4

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
PHENIX(phenix.refine: 1.4_162)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→19.851 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 4855 5.1 %
Rwork0.1918 --
all0.1935 95145 -
obs0.1935 95145 97.61 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.192 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0189 Å20 Å2-2.4666 Å2
2--3.8683 Å20 Å2
3----4.8872 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 39 673 6277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175858
X-RAY DIFFRACTIONf_angle_d1.3867967
X-RAY DIFFRACTIONf_dihedral_angle_d15.4692184
X-RAY DIFFRACTIONf_chiral_restr0.096809
X-RAY DIFFRACTIONf_plane_restr0.0051028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.76990.3221460.2856305098
1.7699-1.79070.28531640.2772299098
1.7907-1.81250.28381740.265300798
1.8125-1.83540.28711450.256306198
1.8354-1.85960.29841720.2475299298
1.8596-1.8850.28821640.2408303598
1.885-1.91190.28521550.241301298
1.9119-1.94040.26741830.2329299998
1.9404-1.97070.25461670.2259304099
1.9707-2.0030.24891860.197299899
2.003-2.03750.21521690.1991303398
2.0375-2.07450.23771600.1937302498
2.0745-2.11440.23771630.1879299598
2.1144-2.15750.21521390.1892308798
2.1575-2.20440.24791670.1857298099
2.2044-2.25560.22961580.1853308498
2.2556-2.31190.20741590.1843298298
2.3119-2.37430.21351320.1845306898
2.3743-2.44410.21971750.1816304998
2.4441-2.52280.22711850.1872298998
2.5228-2.61280.25961440.1902304198
2.6128-2.71710.23391900.1891297798
2.7171-2.84050.24961560.1914302598
2.8405-2.98970.21721490.1908304598
2.9897-3.17630.2241590.1838299597
3.1763-3.42040.22151580.1821300097
3.4204-3.76250.19911600.1693302597
3.7625-4.30220.17521470.1482295996
4.3022-5.40210.16491620.1383295295
5.4021-19.8520.22131670.2157279689
Refinement TLS params.Method: refined / Origin x: 6.5805 Å / Origin y: 22.1674 Å / Origin z: 48.7935 Å
111213212223313233
T0.034 Å2-0.0035 Å2-0.0036 Å2-0.0371 Å2-0.0145 Å2--0.0547 Å2
L0.4724 °20.0341 °2-0.3313 °2-0.08 °20.05 °2--0.7075 °2
S0.0174 Å °0.0028 Å °0.024 Å °0.0041 Å °-0.0089 Å °0.0074 Å °0.0163 Å °-0.0159 Å °-0.0046 Å °
Refinement TLS groupSelection details: all

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