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- PDB-6ek6: Crystal structure of KDM5B in complex with S49195a. -

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Basic information

Entry
Database: PDB / ID: 6ek6
TitleCrystal structure of KDM5B in complex with S49195a.
ComponentsLysine-specific demethylase 5B,Lysine-specific demethylase 5B
KeywordsOXIDOREDUCTASE / KDM5B
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-90V / : / NICKEL (II) ION / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSrikannathasan, V. / Szykowska, A. / Newman, J.A. / Ruda, G.F. / Strain-Damerell, C. / Burgess-Brown, N.A. / Vazquez-Rodriguez, S. / Wright, M. / Brennan, P.E. / Arrowsmith, C.H. ...Srikannathasan, V. / Szykowska, A. / Newman, J.A. / Ruda, G.F. / Strain-Damerell, C. / Burgess-Brown, N.A. / Vazquez-Rodriguez, S. / Wright, M. / Brennan, P.E. / 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 S49195a.
Authors: Srikannathasan, V.
History
DepositionSep 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 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: Lysine-specific demethylase 5B,Lysine-specific demethylase 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,94216
Polymers52,7261
Non-polymers1,21615
Water3,783210
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint29 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.410, 141.410, 150.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-808-

DMS

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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: 52725.555 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 , 7 types, 225 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.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-90V / N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide


Mass: 290.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 70.48 %
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: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.05→64.03 Å / Num. obs: 56258 / % possible obs: 100 % / Redundancy: 19.6 % / Net I/σ(I): 18.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.125 / Num. unique obs: 4073 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A1F

5a1f


Resolution: 2.05→56.742 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.4
RfactorNum. reflection% reflection
Rfree0.2004 2875 5.12 %
Rwork0.1794 --
obs0.1805 56193 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.82 Å2 / Biso mean: 45.0013 Å2 / Biso min: 21.14 Å2
Refinement stepCycle: final / Resolution: 2.05→56.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 68 210 3847
Biso mean--55.61 52.95 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083767
X-RAY DIFFRACTIONf_angle_d0.8675121
X-RAY DIFFRACTIONf_chiral_restr0.051550
X-RAY DIFFRACTIONf_plane_restr0.006667
X-RAY DIFFRACTIONf_dihedral_angle_d5.3413066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.08360.28671290.2724942623
2.0836-2.11960.29751330.261424822615
2.1196-2.15810.28641410.251224972638
2.1581-2.19960.2771250.243425122637
2.1996-2.24450.25711180.233625252643
2.2445-2.29330.27231260.210224952621
2.2933-2.34670.22751710.208924652636
2.3467-2.40540.22031270.205825272654
2.4054-2.47040.20451280.192624982626
2.4704-2.54310.20861400.186825262666
2.5431-2.62520.19791390.192525042643
2.6252-2.7190.22851630.188825052668
2.719-2.82790.21161270.202425362663
2.8279-2.95660.21451330.191825262659
2.9566-3.11240.20961500.185825162666
3.1124-3.30740.25231460.189425542700
3.3074-3.56270.21291130.182825762689
3.5627-3.92120.15711330.155425792712
3.9212-4.48840.15231450.135725842729
4.4884-5.65410.15871460.14226272773
5.6541-56.76340.21021420.187327902932
Refinement TLS params.Method: refined / Origin x: 76.0883 Å / Origin y: 66.2495 Å / Origin z: 11.4468 Å
111213212223313233
T0.1881 Å2-0.0222 Å20.0115 Å2-0.3531 Å2-0.0298 Å2--0.2283 Å2
L0.9523 °20.0233 °2-0.1244 °2-0.3083 °2-0.0703 °2---0.0662 °2
S-0.0622 Å °-0.0014 Å °0.0216 Å °-0.022 Å °0.045 Å °0.0142 Å °0.0041 Å °0.0284 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 754
2X-RAY DIFFRACTION1allA800 - 802
3X-RAY DIFFRACTION1allB1 - 63
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allW1 - 273
6X-RAY DIFFRACTION1allD1
7X-RAY DIFFRACTION1allD2
8X-RAY DIFFRACTION1allD3 - 4
9X-RAY DIFFRACTION1allE1 - 3
10X-RAY DIFFRACTION1allE4 - 7
11X-RAY DIFFRACTION1allF1 - 198
12X-RAY DIFFRACTION1allG3 - 187

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