6K00 | pdb_00006k00

Crystal structure A of ceNAP1-H2A-H2B complex

PDB DOI: https://doi.org/10.2210/pdb6K00/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: 2.20 Å
R-Value Free:
0.243 (Depositor), 0.218 (DCC)
R-Value Work:
0.211 (Depositor), 0.213 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of xlH2A-H2B

(2019) Structure

Macromolecule Content

Total Structure Weight: 92.63 kDa
Atom Count: 5,636
Modeled Residue Count: 712
Deposited Residue Count: 823
Unique protein chains: 2

Macromolecules

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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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P04255 P09588
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.243 (Depositor), 0.218 (DCC)
R-Value Work: 0.211 (Depositor), 0.213 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.298	α = 90
b = 78.724	β = 90
c = 169.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	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.