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- PDB-5oy7: Structure of the 4_601_157 tetranucleosome (P1 form) -

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Basic information

Entry
Database: PDB / ID: 5oy7
TitleStructure of the 4_601_157 tetranucleosome (P1 form)
Components
  • (DNA (619-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
KeywordsGENE REGULATION / nucleosome / histone / DNA / tetranucleosome / chromatin fiber
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 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 ...: / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A / Histone H3
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 5.774 Å
AuthorsEkundayo, B. / Richmond, T.J. / Schalch, T.
Funding support Switzerland, 4items
OrganizationGrant numberCountry
Swiss National Science FoundationP00P3-139137 Switzerland
Swiss National Science FoundationPP00P3_163760 Switzerland
Swiss National Science FoundationPP00P3_172904 Switzerland
European Research CouncilGrant FP/2007-2013/Agreement 322778 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 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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
L: Histone H2B 1.1
M: Histone H3
N: Histone H4
O: Histone H2A
P: Histone H2B 1.1
Q: Histone H3
R: Histone H4
I: Histone H3
J: Histone H4
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
K: Histone H2A
S: Histone H2A
T: Histone H2B 1.1
U: Histone H3
V: Histone H4
W: Histone H2A
X: Histone H2B 1.1
Y: Histone H3
Z: Histone H4
a: Histone H2A
b: Histone H2B 1.1
c: Histone H3
d: Histone H4
e: Histone H2A
f: Histone H2B 1.1
g: DNA (619-MER)
h: DNA (619-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)827,37242
Polymers827,08834
Non-polymers2848
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area232460 Å2
ΔGint-1616 kcal/mol
Surface area298420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.624, 161.465, 227.915
Angle α, β, γ (deg.)78.94, 83.86, 83.74
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 32 molecules LPDHTXbfMQIAEUYcNRJBFVZdOCGKSWae

#1: Protein
Histone H2B 1.1 / H2B1.1


Mass: 13979.291 Da / Num. of mol.: 8
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
#2: Protein
Histone H3


Mass: 15303.930 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h3g, H3l / Production host: Escherichia coli (E. coli) / References: UniProt: Q92133, UniProt: P84233*PLUS
#3: Protein
Histone H4


Mass: 11263.231 Da / Num. of mol.: 8
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
#4: Protein
Histone H2A


Mass: 14109.436 Da / Num. of mol.: 8
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

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DNA chain , 2 types, 2 molecules gh

#5: DNA chain DNA (619-MER)


Mass: 194770.531 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 (619-MER)


Mass: 195070.594 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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Non-polymers , 1 types, 8 molecules

#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl

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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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodyalte, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5.77→141.5 Å / Num. obs: 24331 / % possible obs: 93.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 229.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.076 / Net I/σ(I): 4.9
Reflection shellHighest resolution: 5.77 Å / Mean I/σ(I) obs: 1.63 / Num. unique all: 3457 / Num. unique obs: 4652 / CC1/2: 0.571 / Rrim(I) all: 0.506 / % possible all: 82

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZ0

3lz0


Resolution: 5.774→111.407 Å / SU ML: 0.91 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 28.53
RfactorNum. reflection% reflection
Rfree0.2382 1226 5.04 %
Rwork0.2189 --
obs0.2199 24322 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 5.774→111.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23828 25379 8 0 49215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952660
X-RAY DIFFRACTIONf_angle_d1.46276478
X-RAY DIFFRACTIONf_dihedral_angle_d31.54921747
X-RAY DIFFRACTIONf_chiral_restr0.0828714
X-RAY DIFFRACTIONf_plane_restr0.0045378

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