2NQB | pdb_00002nqb

Drosophila Nucleosome Structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.254 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.224 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Comparative analysis of nucleosome structures from different species.

Chakravarthy, S., Luger, K.

To be published.

Macromolecule Content 

  • Total Structure Weight: 197.35 kDa 
  • Atom Count: 12,294 
  • Modeled Residue Count: 1,054 
  • Deposited Residue Count: 1,260 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3C [auth A],
G [auth E]		135Drosophila melanogasterMutation(s): 0 
Gene Names: His4
UniProt
Find proteins for P02299 (Drosophila melanogaster)
Explore P02299 
Go to UniProtKB:  P02299
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UniProt GroupP02299
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]		103Drosophila melanogasterMutation(s): 0 
Gene Names: His2A
UniProt
Find proteins for P84040 (Drosophila melanogaster)
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Go to UniProtKB:  P84040
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UniProt GroupP84040
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G]		123Drosophila melanogasterMutation(s): 0 
Gene Names: His2B
UniProt
Find proteins for P84051 (Drosophila melanogaster)
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Go to UniProtKB:  P84051
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UniProt GroupP84051
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Reference Sequence
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|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2BF [auth D],
J [auth H]		123Drosophila melanogasterMutation(s): 1 
UniProt
Find proteins for P02283 (Drosophila melanogaster)
Explore P02283 
Go to UniProtKB:  P02283
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UniProt GroupP02283
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Reference Sequence
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(by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
alpha-satellite DNAA [auth I],
B [auth J]		146Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.224 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.143α = 90
b = 109.581β = 90
c = 182.045γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description