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- PDB-5oxv: Structure of the 4_601_157 tetranucleosome (C2 form) -

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Basic information

Entry
Database: PDB / ID: 5oxv
TitleStructure of the 4_601_157 tetranucleosome (C2 form)
Components
  • DNA STRAND 1 (601-based sequence model)
  • DNA STRAND 2 (601-based sequence model)
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsGENE REGULATION / nucleosome / histone / DNA / tetranucleosome / chromatin fiber
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
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 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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciessynthetic construct (others)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.721 Å
AuthorsEkundayo, B. / Schalch, T.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3-139137 Switzerland
Swiss National Science FoundationPP00P3_163760 Switzerland
Swiss National Science FoundationPP00P3_172904 Switzerland
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Capturing Structural Heterogeneity in Chromatin Fibers.
Authors: Ekundayo, B. / Richmond, T.J. / Schalch, T.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / pdbx_validate_symm_contact ...pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.3Jan 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
J: DNA STRAND 1 (601-based sequence model)
R: Histone H2B 1.1
Q: Histone H2A
P: Histone H4
O: Histone H3.2
N: Histone H2B 1.1
M: Histone H2A
L: Histone H4
K: Histone H3.2
I: DNA STRAND 2 (601-based sequence model)
H: Histone H2B 1.1
G: Histone H2A
F: Histone H4
E: Histone H3.2
D: Histone H2B 1.1
C: Histone H2A
B: Histone H4
A: Histone H3.2


Theoretical massNumber of molelcules
Total (without water)411,65718
Polymers411,65718
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, the tetranucleosome arrays run at the expected size
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area115790 Å2
ΔGint-753 kcal/mol
Surface area149470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)348.839, 63.274, 271.361
Angle α, β, γ (deg.)90.00, 124.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA chain , 2 types, 2 molecules JI

#1: DNA chain DNA STRAND 1 (601-based sequence model)


Mass: 96886.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA STRAND 2 (601-based sequence model)


Mass: 96147.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Protein , 4 types, 16 molecules RNHDQMGCPLFBOKEA

#2: Protein
Histone H2B 1.1 / H2B1.1


Mass: 13979.291 Da / Num. of mol.: 4
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
#3: Protein
Histone H2A


Mass: 14109.436 Da / Num. of mol.: 4
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, UniProt: P06897*PLUS
#4: Protein
Histone H4


Mass: 11263.231 Da / Num. of mol.: 4
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
#5: Protein
Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 4
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

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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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodylate, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 6.72→200 Å / Num. obs: 9194 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.163 / Net I/σ(I): 5.8
Reflection shellResolution: 6.72→7.51 Å / Redundancy: 7.4 % / Rmerge(I) obs: 4.943 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2554 / CC1/2: 0.164 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSVERSION May 1, 2016 BUILT=20160617data reduction
Aimless0.5.21data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZ0

3lz0


Resolution: 6.721→71.666 Å / SU ML: 1.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 58.89
RfactorNum. reflection% reflection
Rfree0.3522 1016 12.63 %
Rwork0.317 --
obs0.3208 8045 87.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 6.721→71.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11918 12730 0 0 24648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00926353
X-RAY DIFFRACTIONf_angle_d1.47238268
X-RAY DIFFRACTIONf_dihedral_angle_d31.65910878
X-RAY DIFFRACTIONf_chiral_restr0.0834362
X-RAY DIFFRACTIONf_plane_restr0.0042691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.7213-7.07540.4815630.5085394X-RAY DIFFRACTION35
7.0754-7.51820.51791260.4974924X-RAY DIFFRACTION85
7.5182-8.0980.45251480.41781142X-RAY DIFFRACTION99
8.098-8.91160.40761650.40031106X-RAY DIFFRACTION98
8.9116-10.19790.43231740.3841111X-RAY DIFFRACTION99
10.1979-12.83630.38511790.39651147X-RAY DIFFRACTION99
12.8363-71.66970.29861610.2461205X-RAY DIFFRACTION99

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