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- PDB-6ete: Crystal structure of KDM4D with tetrazolhydrazide compound 5 -

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Basic information

Entry
Database: PDB / ID: 6ete
TitleCrystal structure of KDM4D with tetrazolhydrazide compound 5
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / KDM4D / ligand binding / Tetrazolylhydrazide / tetrazole / inhibitor design / cancer / epigenetics
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
Chem-BWK / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.468 Å
AuthorsMalecki, P.H. / Weiss, M.S. / Heinemann, U. / Link, A.
CitationJournal: To be published
Title: Crystal structure of KDM4D with tetrazolylhydrazide ligand NR128
Authors: Malecki, P.H. / Link, A. / Weiss, M.S. / Heinemann, U.
History
DepositionOct 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: 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 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,45914
Polymers39,4921
Non-polymers96813
Water6,323351
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-28 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.464, 71.464, 151.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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


Mass: 39491.793 Da / Num. of mol.: 1 / Fragment: JMJD2D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6B0I6, 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, 364 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.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-BWK / [2-(1-methyl-1,2,3,4-tetrazol-4-ium-5-yl)ethanoylamino]azanium


Mass: 158.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10N6O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2016
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.47→47.923 Å / Num. obs: 127491 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.607 % / Biso Wilson estimate: 18.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.049 / Χ2: 1.146 / Net I/σ(I): 18.16 / Num. measured all: 587371
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.47-1.564.5390.6942.029315920673205230.6850.78799.3
1.56-1.664.6490.4113.59034219438194330.8650.465100
1.66-1.84.4580.2325.958046718069180520.9490.26599.9
1.8-1.974.6050.1211.277638016600165850.9850.13699.9
1.97-2.24.7850.06820.027188215024150220.9950.076100
2.2-2.544.510.04528.385986913286132760.9970.05199.9
2.54-3.114.6940.03140.325246211195111770.9990.03599.8
3.11-4.394.6990.02356.2140666866586550.9990.02699.9
4.39-47.9234.6440.02162.2722144479547680.9990.02399.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.468→35.732 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1534 2081 1.63 %
Rwork0.1276 125406 -
obs0.128 127487 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.57 Å2 / Biso mean: 27.331 Å2 / Biso min: 8.91 Å2
Refinement stepCycle: final / Resolution: 1.468→35.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 104 363 3154
Biso mean--49.21 41.93 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0313074
X-RAY DIFFRACTIONf_angle_d2.3624205
X-RAY DIFFRACTIONf_chiral_restr0.166421
X-RAY DIFFRACTIONf_plane_restr0.016558
X-RAY DIFFRACTIONf_dihedral_angle_d15.7191182
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4679-1.50210.26681370.22548207834498
1.5021-1.53960.21131360.197384258561100
1.5396-1.58120.21461410.177783588499100
1.5812-1.62780.21041390.157984098548100
1.6278-1.68030.16691360.146183328468100
1.6803-1.74040.17181430.135384008543100
1.7404-1.810.1671390.126282838422100
1.81-1.89240.13471410.112884098550100
1.8924-1.99220.16191430.107383658508100
1.9922-2.1170.11771410.108383758516100
2.117-2.28040.15981390.107583828521100
2.2804-2.50980.13861380.116583618499100
2.5098-2.87290.1351340.121883708504100
2.8729-3.6190.12511420.124683648506100
3.619-35.74260.17061320.132783668498100

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