6K09 | pdb_00006k09

Crystal structure B of ceNAP1-H2A-H2B complex

• PDB DOI: https://doi.org/10.2210/pdb6K09/pdb

• Classification: CHAPERONE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2019-05-05 Released: 2019-10-09 
• Deposition Author(s): Liu, Y.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.248 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of xlH2A-H2B

Liu, Y.R.

(2019) Structure 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 92.63 kDa 
• Atom Count: 5,716 
• Modeled Residue Count: 715 
• Deposited Residue Count: 823 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome Assembly Protein	A, B	308	Caenorhabditis elegans	Mutation(s): 0  Gene Names: nap-1
UniProt
Find proteins for Q19007 (Caenorhabditis elegans) Explore Q19007  Go to UniProtKB:  Q19007

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1,Histone H2A	C [auth D]	207	Caenorhabditis elegans	Mutation(s): 0
UniProt
Find proteins for P04255 (Caenorhabditis elegans) Explore P04255  Go to UniProtKB:  P04255
Find proteins for P09588 (Caenorhabditis elegans) Explore P09588  Go to UniProtKB:  P09588
UniProt Groups	P04255P09588

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.248 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.795	α = 90
b = 79.18	β = 90
c = 172.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Liu, Y.R.

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Refinement description