5EG6 | pdb_00005eg6

CSL-RITA complex bound to DNA

PDB DOI: https://doi.org/10.2210/pdb5EG6/pdb
NAKB: 5EG6

Classification: TRANSCRIPTION/DNA BINDING PROTEIN/DNA
Organism(s): synthetic construct, Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-10-26 Released: 2017-04-26
Deposition Author(s): Tabaja, N.H., Kovall, R.A.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

CSL-RITA complex bound to DNA

Tabaja, N.H., Kovall, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 60.61 kDa
Atom Count: 4,285
Modeled Residue Count: 459
Deposited Residue Count: 468
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombining binding protein suppressor of hairless	B [auth C]	422	Mus musculus	Mutation(s): 0 Gene Names: Rbpj, Igkjrb1, Igkrsbp, Rbpsuh
UniProt & NIH Common Fund Data Resources
Find proteins for P31266 (Mus musculus) Explore P31266 Go to UniProtKB: P31266
IMPC: MGI:96522
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31266
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
hRITA	C [auth R]	16	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q96K30 (Homo sapiens) Explore Q96K30 Go to UniProtKB: Q96K30
PHAROS: Q96K30 GTEx: ENSG00000139405
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96K30
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(APAPTPCPTPTPTPCPCPCPAPCPAPGP*T)-3')	A [auth B]	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(TPTPAPCPTPGPTPGPGPGPAPAPAPGP*A)-3')	D [auth A]	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BU1 Query on BU1 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain W [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain W [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain W [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] W [auth C] X [auth C] AA [auth C], BA [auth C], CA [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth R] SDF format, chain E [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth C] SDF format, chain P [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth C] SDF format, chain I [auth C] SDF format, chain F [auth C] MOL2 format, chain DA [auth R] MOL2 format, chain E [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth C] MOL2 format, chain I [auth C] MOL2 format, chain F [auth C] mmCIF format, chain DA [auth R] mmCIF format, chain E [auth C] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth C] mmCIF format, chain I [auth C] mmCIF format, chain F [auth C]	DA [auth R] E [auth C] F [auth C] G [auth C] H [auth C] DA [auth R], E [auth C], F [auth C], G [auth C], H [auth C], I [auth C], J [auth C], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth R] Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain DA [auth R] Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.788	α = 90
b = 96.41	β = 90
c = 96.711	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-04-26

Deposition Author(s):

Tabaja, N.H.

Kovall, R.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA178974-02
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	T32CA117846-07