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- PDB-6eiu: Crystal structure of KDM5B in complex with KDOPZ29a -

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Basic information

Entry
Database: PDB / ID: 6eiu
TitleCrystal structure of KDM5B in complex with KDOPZ29a
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-B6T / : / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.88 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 KDOPZ29a.
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)54,64318
Polymers53,2671
Non-polymers1,37617
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint26 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.380, 143.380, 153.820
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: 53267.176 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, 297 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-B6T / 8-oxidanyl-6-phenyl-7-propan-2-yl-imidazo[1,2-b]pyridazine-3-carbonitrile


Mass: 278.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 4.28 Å3/Da / Density % sol: 71.29 %
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: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.83→124.17 Å / Num. obs: 82282 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.1
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 20.8 % / Rmerge(I) obs: 2.858 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6007 / CC1/2: 0.604 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementResolution: 1.88→65.384 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.2209 4063 4.94 %
Rwork0.1957 --
obs0.1969 82204 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.84 Å2 / Biso mean: 43.3288 Å2 / Biso min: 24.44 Å2
Refinement stepCycle: final / Resolution: 1.88→65.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 73 280 3925
Biso mean--49.19 52.06 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083782
X-RAY DIFFRACTIONf_angle_d0.8665144
X-RAY DIFFRACTIONf_chiral_restr0.056553
X-RAY DIFFRACTIONf_plane_restr0.006682
X-RAY DIFFRACTIONf_dihedral_angle_d4.4053064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.83-1.85160.32311200.30626732793
1.8516-1.87410.36331170.29326592776
1.8741-1.89790.28251530.280626532806
1.8979-1.92280.27841490.269626392788
1.9228-1.94920.27431430.263226522795
1.9492-1.9770.29521450.267226362781
1.977-2.00650.2931610.247926332794
2.0065-2.03790.27071560.231226512807
2.0379-2.07130.24571530.218526322785
2.0713-2.1070.21841280.2226942822
2.107-2.14530.26551360.21326612797
2.1453-2.18660.24891310.221326592790
2.1866-2.23120.22341570.222926632820
2.2312-2.27980.24621360.220426702806
2.2798-2.33280.26191310.20626722803
2.3328-2.39110.22711530.210426882841
2.3911-2.45580.2471390.20426472786
2.4558-2.52810.23591330.201526902823
2.5281-2.60970.23761570.199426892846
2.6097-2.70290.20191340.208226852819
2.7029-2.81120.2151590.204326822841
2.8112-2.93910.26031360.202826862822
2.9391-3.0940.24681310.206227342865
3.094-3.28790.21361380.204727242862
3.2879-3.54170.20231340.193327202854
3.5417-3.89810.18791230.17527722895
3.8981-4.46210.1921320.157227742906
4.4621-5.62130.16641240.153128302954
5.6213-65.42560.21771540.196729733127
Refinement TLS params.Method: refined / Origin x: 77.2703 Å / Origin y: 66.7046 Å / Origin z: 11.6379 Å
111213212223313233
T0.2296 Å2-0.0157 Å20.0257 Å2-0.3838 Å2-0.0314 Å2--0.2852 Å2
L1.4791 °20.1879 °20.2675 °2-0.3328 °2-0.0568 °2--0.2194 °2
S-0.0295 Å °0.0451 Å °0.089 Å °-0.0122 Å °0.0225 Å °0.0312 Å °-0.0036 Å °0.0687 Å °-0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 754
2X-RAY DIFFRACTION1allA800 - 801
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allD1 - 110
6X-RAY DIFFRACTION1allE1 - 4
7X-RAY DIFFRACTION1allE5 - 6
8X-RAY DIFFRACTION1allE7
9X-RAY DIFFRACTION1allF1 - 3
10X-RAY DIFFRACTION1allF4 - 5
11X-RAY DIFFRACTION1allW1 - 358
12X-RAY DIFFRACTION1allG1

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