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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.279 (Depositor), 0.233 (DCC)
R-Value Work:
0.250 (Depositor)
R-Value Observed:
0.252 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6K02

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of xlH2A-H2B

(2019) Structure

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q19007
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.279 (Depositor), 0.233 (DCC)
R-Value Work: 0.250 (Depositor)
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

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Entry History

Deposition Data

Released Date: 2019-10-09

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.