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- PDB-2fj7: Crystal structure of Nucleosome Core Particle Containing a Poly (... -

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Basic information

Entry
Database: PDB / ID: 2fj7
TitleCrystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element
Components
  • (147 bp DNA containing 16 bp poly ...) x 2
  • Histone H2B
  • Histone H4
  • histone H2A
  • histone H3
KeywordsSTRUCTURAL PROTEIN/DNA / Protein-DNA complex / narrow minor groove / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / nucleosome assembly / 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. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBao, Y. / White, C.L. / Luger, K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Nucleosome Core Particles Containing a Poly(dA.dT) Sequence Element Exhibit a Locally Distorted DNA Structure.
Authors: Bao, Y. / White, C.L. / Luger, K.
History
DepositionDec 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: 147 bp DNA containing 16 bp poly dA element
J: 147 bp DNA containing 16 bp poly dT element
A: histone H3
B: Histone H4
C: histone H2A
D: Histone H2B
E: histone H3
F: Histone H4
G: histone H2A
H: Histone H2B


Theoretical massNumber of molelcules
Total (without water)199,50610
Polymers199,50610
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.918, 109.598, 177.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHistone octomer and the 147 bp DNA containing Poly (dA.dT) element were reconstituted to form NCP, which is the biological unit.

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Components

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147 bp DNA containing 16 bp poly ... , 2 types, 2 molecules IJ

#1: DNA chain 147 bp DNA containing 16 bp poly dA element


Mass: 45369.137 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 147 bp DNA containing 16 bp poly dT element


Mass: 45350.035 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 4 types, 8 molecules AEBFCGDH

#3: Protein histone H3


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: GenBank: 30268544, UniProt: P84233*PLUS
#4: 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
#5: Protein histone H2A


Mass: 13978.241 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: GenBank: 30268540, UniProt: P06897*PLUS
#6: 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: P02281

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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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20 to 35 mM KCl, 34 to 48 mM MnCl2, and 5mM K-cacodylate pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2MnCl211
3cacodylate11
4H2O11
5KCl12
6MnCl212
7cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1271 Å
DetectorDate: Jun 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 34730 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.067 / Χ2: 4.041
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.226 / Num. unique all: 3428 / Χ2: 1.54 / % possible all: 99.8

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.346 / Packing: 0.474
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct98.2 0
Translation4 Å15 Ågeneral98.2 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→50 Å
RfactorNum. reflection% reflection
Rfree0.35 1653 -
Rwork0.28 --
all-34557 -
obs-32887 95.2 %
Displacement parametersBiso mean: 126.347 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6017 6021 0 0 12038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.3542

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