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- PDB-6ej0: Crystal structure of KDM5B in complex with KDOPZ000049a. -

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Basic information

Entry
Database: PDB / ID: 6ej0
TitleCrystal structure of KDM5B in complex with KDOPZ000049a.
ComponentsLysine-specific demethylase 5B,Lysine-specific demethylase 5B
KeywordsOXIDOREDUCTASE / KDM5B Lysine specific demethylase
Function / homology
Function and homology information


regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus ...regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus / branching involved in mammary gland duct morphogenesis / single fertilization / histone demethylase activity / response to fungicide / cellular response to leukemia inhibitory factor / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / transcription corepressor activity / rhythmic process / sequence-specific double-stranded DNA binding / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain ...: / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-B7K / : / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.06 Å
AuthorsSrikannathasan, V. / Newman, J.A. / Szykowska, A. / Wright, M. / Ruda, G.F. / Vazquez-Rodriguez, S.A. / Kupinska, K. / Strain-Damerell, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. ...Srikannathasan, V. / Newman, J.A. / Szykowska, A. / Wright, M. / Ruda, G.F. / Vazquez-Rodriguez, S.A. / Kupinska, K. / Strain-Damerell, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Oppermann, U. / Huber, K. / von Delft, F.
CitationJournal: to be published
Title: Crystal structure of KDM5B in complex with KDOPZ000049a.
Authors: srikannathasan, v.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 5B,Lysine-specific demethylase 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,95012
Polymers52,8551
Non-polymers1,09611
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint7 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.820, 141.820, 151.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 5B,Lysine-specific demethylase 5B / Cancer/testis antigen 31 / CT31 / Histone demethylase JARID1B / Jumonji/ARID domain-containing ...Cancer/testis antigen 31 / CT31 / Histone demethylase JARID1B / Jumonji/ARID domain-containing protein 1B / PLU-1 / Retinoblastoma-binding protein 2 homolog 1 / RBP2-H1


Mass: 52854.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM5B, JARID1B, PLU1, RBBP2H1 / Plasmid: PFB-LIC-BSE / Cell (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UGL1, 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 , 6 types, 188 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-B7K / 7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile


Mass: 405.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N7O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.8M Pottassium Phosphate-dibasic, 0.8M Sodium Phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→64.24 Å / Num. obs: 56074 / % possible obs: 100 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 21.6
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 20 % / Rmerge(I) obs: 2.416 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4074 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementResolution: 2.06→51.807 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 22.73
Details: undefined side chains removed. residues without density deleted.
RfactorNum. reflection% reflection
Rfree0.2104 2869 5.12 %
Rwork0.1903 --
obs0.1914 56007 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.77 Å2 / Biso mean: 56.8936 Å2 / Biso min: 28.27 Å2
Refinement stepCycle: final / Resolution: 2.06→51.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3599 0 61 177 3837
Biso mean--67.75 58.18 -
Num. residues----453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083794
X-RAY DIFFRACTIONf_angle_d0.9795166
X-RAY DIFFRACTIONf_chiral_restr0.061551
X-RAY DIFFRACTIONf_plane_restr0.006691
X-RAY DIFFRACTIONf_dihedral_angle_d5.4823098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.06-2.09550.28061360.273926032739
2.0955-2.13360.32641350.276226202755
2.1336-2.17470.30431620.263226012763
2.1747-2.21910.31231180.254726322750
2.2191-2.26730.28191260.247526142740
2.2673-2.32010.25721520.238426092761
2.3201-2.37810.28991570.226426072764
2.3781-2.44240.26631250.228626532778
2.4424-2.51430.25441460.216326102756
2.5143-2.59540.24711440.21426452789
2.5954-2.68820.24611660.21725832749
2.6882-2.79580.25211470.215326582805
2.7958-2.9230.24241430.211426422785
2.923-3.07710.24431440.213426602804
3.0771-3.26990.25171520.208326362788
3.2699-3.52230.25731290.198827052834
3.5223-3.87660.14961330.173226862819
3.8766-4.43730.16291500.149227172867
4.4373-5.58950.15241570.149227362893
5.5895-51.82370.19931470.18129213068
Refinement TLS params.Method: refined / Origin x: 76.4595 Å / Origin y: 66.2565 Å / Origin z: 11.627 Å
111213212223313233
T0.2559 Å2-0.0382 Å20.0352 Å2-0.4181 Å2-0.0465 Å2--0.2753 Å2
L2.2761 °20.1116 °20.1813 °2-0.3807 °2-0.1275 °2--0.0055 °2
S-0.0176 Å °0.0086 Å °0.0794 Å °-0.0186 Å °0.0262 Å °0.0399 Å °0.0157 Å °0.0495 Å °-0.003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 754
2X-RAY DIFFRACTION1allA800 - 801
3X-RAY DIFFRACTION1allB1 - 2
4X-RAY DIFFRACTION1allC1 - 2
5X-RAY DIFFRACTION1allC3 - 5
6X-RAY DIFFRACTION1allE1
7X-RAY DIFFRACTION1allF1
8X-RAY DIFFRACTION1allS1 - 177

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