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- PDB-4d6r: crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE... -

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Basic information

Entry
Database: PDB / ID: 4d6r
Titlecrystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound o-toluenesulfonamide
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4D
KeywordsTRANSCRIPTION / KDM4D / FLJ10251 / MGC141909 / DEMETHYLASE/2OG / JUMONJI DOMAIN CONTAINING 2D
Function / homology
Function and homology information


positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / 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
O-TOLUENESULFONAMIDE / NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 Å
AuthorsKrojer, T. / Vollmar, M. / Bradley, A. / Crawley, L. / Szykowska, A. / Burgess-Brown, N. / Gileadi, C. / Johansson, C. / Oppermann, U. / Bountra, C. ...Krojer, T. / Vollmar, M. / Bradley, A. / Crawley, L. / Szykowska, A. / Burgess-Brown, N. / Gileadi, C. / Johansson, C. / Oppermann, U. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: To be Published
Title: Crystal Structure of Human Jmjd2D in Complex with N-Oxalylglycine and Bound O-Toluenesulfonamide
Authors: Krojer, T. / Vollmar, M. / Bradley, A. / Crawley, L. / Szykowska, A. / Burgess-Brown, N. / Gileadi, C. / Johansson, C. / Oppermann, U. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
History
DepositionNov 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSINE-SPECIFIC DEMETHYLASE 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,61211
Polymers39,5791
Non-polymers1,03310
Water7,656425
1
A: LYSINE-SPECIFIC DEMETHYLASE 4D
hetero molecules

A: LYSINE-SPECIFIC DEMETHYLASE 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,22422
Polymers79,1582
Non-polymers2,06620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4890 Å2
ΔGint-6 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.514, 71.514, 150.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21A-2282-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 4D / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D / JUMONJI DOMAIN-CONTAINING PROTEIN 2D / JMJD2D


Mass: 39578.867 Da / Num. of mol.: 1 / Fragment: JUMONJI DOMAIN, RESIDUES 1-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6B0I6

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Non-polymers , 6 types, 435 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Chemical ChemComp-IEJ / O-TOLUENESULFONAMIDE


Mass: 171.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H9NO2S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.47 Å3/Da / Density % sol: 50.24 % / Description: NONE
Crystal growpH: 7
Details: 28% PEG3350, 0.1M HEPES PH 7.0, 0.2M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Dec 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.4→29.43 Å / Num. obs: 77903 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 12.65 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.3 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.398→29.432 Å / SU ML: 0.1 / σ(F): 1.36 / Phase error: 14.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1723 3894 5 %
Rwork0.1448 --
obs0.1462 77806 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.398→29.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 61 425 3078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072938
X-RAY DIFFRACTIONf_angle_d1.0844013
X-RAY DIFFRACTIONf_dihedral_angle_d12.1861097
X-RAY DIFFRACTIONf_chiral_restr0.047400
X-RAY DIFFRACTIONf_plane_restr0.006558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3975-1.41460.2361390.18212479X-RAY DIFFRACTION95
1.4146-1.43250.19721390.16312604X-RAY DIFFRACTION100
1.4325-1.45130.18511440.15572575X-RAY DIFFRACTION100
1.4513-1.47120.19771400.15392601X-RAY DIFFRACTION100
1.4712-1.49220.21211360.14362611X-RAY DIFFRACTION100
1.4922-1.51450.18711240.13892623X-RAY DIFFRACTION100
1.5145-1.53820.17491550.12962586X-RAY DIFFRACTION100
1.5382-1.56340.19541320.1252601X-RAY DIFFRACTION100
1.5634-1.59030.17731330.12882642X-RAY DIFFRACTION100
1.5903-1.61920.17281250.12092598X-RAY DIFFRACTION100
1.6192-1.65040.1571330.1242629X-RAY DIFFRACTION100
1.6504-1.68410.17881260.12672609X-RAY DIFFRACTION100
1.6841-1.72070.16771330.12622623X-RAY DIFFRACTION100
1.7207-1.76070.16471580.12732609X-RAY DIFFRACTION100
1.7607-1.80470.17051370.12562628X-RAY DIFFRACTION100
1.8047-1.85350.14271400.12522624X-RAY DIFFRACTION100
1.8535-1.90810.16641370.12812639X-RAY DIFFRACTION100
1.9081-1.96960.17091480.13162631X-RAY DIFFRACTION100
1.9696-2.040.16551480.12962617X-RAY DIFFRACTION100
2.04-2.12170.14751320.13312645X-RAY DIFFRACTION100
2.1217-2.21820.13761130.13432686X-RAY DIFFRACTION100
2.2182-2.33510.16761320.14142661X-RAY DIFFRACTION100
2.3351-2.48130.16161780.14522628X-RAY DIFFRACTION100
2.4813-2.67280.16871290.15132690X-RAY DIFFRACTION100
2.6728-2.94150.18041530.15742676X-RAY DIFFRACTION100
2.9415-3.36670.15791610.14872699X-RAY DIFFRACTION100
3.3667-4.23960.16831340.14782769X-RAY DIFFRACTION100
4.2396-29.43810.21081350.17772929X-RAY DIFFRACTION100

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