OCA Atlas for 3WKJ

3WKJ

Structural Protein Dna

date

Oct 22, 2013

title

The Nucleosome Containing Human Tsh2b

authors

T.Urahama, N.Horikoshi, A.Osakabe, H.Tachiwana, H.Kurumizaka

compound

source

Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3a, Histone H3b, Histone H3c, Histone Histone H3f, Histone H3h, Histone H3i, Histone H3j, His Histone H3l;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H2a Type 1-Be
Chain: C, G
Synonym: Histone H2a.2, Histone H2aa, Histone H2am
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

Molecule: Histone H2b Type 1-A
Chain: D, H
Synonym: Histone H2b, Testis, Tsh2b.1, Testis-Specific Hist
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ba, Tsh2b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

Molecule: Dna (145-Mer)
Chain: I, J
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5-Alpha
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T Easy

symmetry

Space Group: P 21 21 21

R_factor

0.235

R_Free

0.291

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
107.037	109.926	182.961	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.80 Å

ligand

CL, MN

enzyme

Gene
Ontology

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

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (242 Kb) [Save to disk]

Biological Unit Coordinates (3wkj.pdb1.gz) 235 Kb

LPC: Ligand-Protein Contacts for 3WKJ

CSU: Contacts of Structural Units for 3WKJ

Structure Factors (453 Kb)

Retrieve 3WKJ in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3WKJ from S2C, [Save to disk]

Re-refined 3wkj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3WKJ 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 3WKJ

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

3D motif for 3WKJ, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3wkj_I] [3wkj] [3wkj_A] [3wkj_B] [3wkj_E] [3wkj_G] [3wkj_F] [3wkj_J] [3wkj_D] [3wkj_H] [3wkj_C]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 3WKJ: [H2A] [H2B] [H3] [H4 ] by SMART

Other resources with information on 3WKJ

Community annotation for 3WKJ at PDBWiki (http://pdbwiki.org)

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