6K02 | pdb_00006k02

Crystal structure of ceNAP1 core

• PDB DOI: https://doi.org/10.2210/pdb6K02/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: 2.16 Å
• R-Value Free: 
  0.279 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

Crystal structure of xlH2A-H2B

Liu, Y.R.

(2019) Structure 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.11 kDa 
• Atom Count: 4,299 
• Modeled Residue Count: 532 
• Deposited Residue Count: 616 
• Unique protein chains: 1

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.279 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.733	α = 90
b = 126.747	β = 90
c = 118.192	γ = 90

Software Package:

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