OCA Atlas for 5ONG

5ONG

Dna Binding Protein

date

Aug 03, 2017

title

X-Ray Crystal Structure Of A Nucleosome Core Particle With I Site-Specifically Crosslinked To The Histone Octamer

authors

T.D.Frouws, P.D.Barth, T.J.Richmond

compound

source

Molecule: Dna (147-Mer)
Chain: I
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Dh10b
Expression_system_vector_type: Plasmid
Expression_system_vector: Puc57

Molecule: Dna (147-Mer)
Chain: J
Engineered: Yes

Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Mutation: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet3a

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Molecule: Histone H2a
Chain: C, G
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet3a

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1
Engineered: Yes

symmetry

Space Group: P 21 21 21

R_factor

0.206

R_Free

0.247

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
106.240	183.130	109.490	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.80 Å

ligand

CL, G47, MN

enzyme

Gene
Ontology

Chain	Function	Process	Component
A, E
C, G
F, B
H, D

Primary reference

Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability., Frouws TD, Barth PD, Richmond TJ, J Mol Biol. 2017 Nov 4. pii: S0022-2836(17)30522-3. doi:, 10.1016/j.jmb.2017.10.029. PMID:29113904

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (522 Kb) [Save to disk]

Biological Unit Coordinates (5ong.pdb1.gz) 506 Kb

LPC: Ligand-Protein Contacts for 5ONG

CSU: Contacts of Structural Units for 5ONG

Structure Factors (386 Kb)

Retrieve 5ONG in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5ONG from S2C, [Save to disk]

View 5ONG in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 5ONG

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5ong_G] [5ong_E] [5ong_D] [5ong_C] [5ong_I] [5ong_H] [5ong_F] [5ong_B] [5ong_J] [5ong_A]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 5ONG

Community annotation for 5ONG at PDBWiki (http://pdbwiki.org)

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