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- PDB-4kgc: Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLEN... -

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Basic information

Entry
Database: PDB / ID: 4kgc
TitleNucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM
Components
  • (DNA (145-mer)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / DNA-protein complex / nucleosome / Ruthenium agents / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-HRU / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsAdhireksan, Z. / Davey, C.A.
CitationJournal: Nat Commun / Year: 2014
Title: Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity
Authors: Adhireksan, Z. / Davey, G.E. / Campomanes, P. / Groessl, M. / Clavel, C.M. / Yu, H. / Nazarov, A.A. / Yeo, C.H. / Ang, W.H. / Droge, P. / Rothlisberger, U. / Dyson, P.J. / Davey, C.A.
History
DepositionApr 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (145-mer)
J: DNA (145-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,79318
Polymers199,29910
Non-polymers1,4948
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58080 Å2
ΔGint-449 kcal/mol
Surface area73100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.620, 109.710, 181.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2


Mass: 15421.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A /


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13979.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-mer)


Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (145-mer)


Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 8 molecules

#7: Chemical
ChemComp-HRU / (ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)cyclohexane-1,2,3,4,5,6-hexayl]ruthenium


Mass: 295.386 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H22N2Ru
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Nonpolymer detailsNCP CRYSTALS WERE SOAKED WITH (ETA6-P-CYMENE)-CHLORO-(1,2-ETHYLENEDIAMINE)-RUTHENIUM(II) ...NCP CRYSTALS WERE SOAKED WITH (ETA6-P-CYMENE)-CHLORO-(1,2-ETHYLENEDIAMINE)-RUTHENIUM(II) HEXAFLUOROPHOSPHATE. UPON BINDING TO NCP ELEMENTS, ONLY (ETA6-P-CYMENE)-(1,2-ETHYLENEDIAMINE)-RUTHENIUM REMAINED.
Sequence detailsUNINTENTIONAL MUTATIONS OR VARIATIONS IN GENOMIC SOURCES

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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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.5 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2011
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.69→60.6 Å / Num. obs: 55781
Reflection shellResolution: 2.69→2.84 Å

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Processing

Software
NameVersionClassification
RemDAqdata collection
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→60.6 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 13.757 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.96 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28234 1143 2.1 %RANDOM
Rwork0.24764 ---
obs0.24835 54577 92.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.444 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2---3.86 Å20 Å2
3---2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.69→60.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6076 5939 76 0 12091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02112917
X-RAY DIFFRACTIONr_angle_refined_deg1.4322.54818762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7165757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37121.338269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.347151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4241584
X-RAY DIFFRACTIONr_chiral_restr0.070.22125
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027705
X-RAY DIFFRACTIONr_mcbond_it0.6591.53797
X-RAY DIFFRACTIONr_mcangle_it1.2726110
X-RAY DIFFRACTIONr_scbond_it1.32839120
X-RAY DIFFRACTIONr_scangle_it2.1984.512556
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 41 -
Rwork0.331 2646 -
obs--61.26 %

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