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- PDB-3kuy: DNA Stretching in the Nucleosome Facilitates Alkylation by an Int... -

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Basic information

Entry
Database: PDB / ID: 3kuy
TitleDNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent
Components
  • (DNA (145-MER)) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / Nucleosome / chromatin / DNA stretching / intercalation / alkylation / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-ATV / : / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A / Histone H2B
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWu, B. / Davey, C.A.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent
Authors: Davey, G.E. / Wu, B. / Dong, Y. / Surana, U. / Davey, C.A.
History
DepositionNov 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (145-MER)
J: DNA (145-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,76413
Polymers196,20310
Non-polymers5613
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57160 Å2
ΔGint-376 kcal/mol
Surface area73530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.161, 109.588, 182.413
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: 15303.930 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: 11263.231 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: 12941.095 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: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B


Mass: 13848.097 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: Q92130, UniProt: P02281*PLUS

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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
#6: DNA chain DNA (145-MER)


Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 2 types, 3 molecules

#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-ATV / 2-[(2R)-oxiran-2-ylmethyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione / N-(2,3-epoxypropyl)-1,8-naphthalimide


Mass: 253.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11NO3

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Details

Sequence detailsTHESE FOUR RESIDUES (A/E ALA 102 AND D/H GLU -1 AND D/H PRO 7 AND D/H THR 29) COULD BE TREATED AS ...THESE FOUR RESIDUES (A/E ALA 102 AND D/H GLU -1 AND D/H PRO 7 AND D/H THR 29) COULD BE TREATED AS UNINTENTIONAL 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6
Details: 85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→54.8 Å / Num. obs: 47896 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.068 / Num. measured all: 356697
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6839 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NZD

2nzd


Resolution: 2.9→53.17 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.912 / SU B: 16.017 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28591 978 2 %RANDOM
Rwork0.238 ---
obs0.23896 46854 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.089 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å20 Å2
2---3.16 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→53.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 5939 39 0 12042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02112865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3892.54518622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9015757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1921.338269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.419151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0531584
X-RAY DIFFRACTIONr_chiral_restr0.0780.22115
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027577
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.25326
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.28063
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2369
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.30.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6051.53865
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0826110
X-RAY DIFFRACTIONr_scbond_it0.99312207
X-RAY DIFFRACTIONr_scangle_it1.8554.512506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 85 -
Rwork0.294 3338 -
obs--98.28 %

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