2XSD

Crystal Structure of the dimeric Oct-6 (Pou3f1) POU domain bound to palindromic MORE DNA

PDB DOI: https://doi.org/10.2210/pdb2XSD/pdb
NAKB: 2XSD

Classification: TRANSCRIPTION/DNA
Organism(s): Mus musculus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-09-28 Released: 2010-10-20
Deposition Author(s): Jauch, R., Choo, S.H., Ng, C.K.L., Kolatkar, P.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.232
R-Value Work: 0.194
R-Value Observed: 0.198

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7XRC

Literature

Crystal Structure of the Dimeric Oct6 (POU3F1) POU Domain Bound to Palindromic More DNA.

Jauch, R., Choo, S.H., Ng, C.K.L., Kolatkar, P.R.

(2011) Proteins 79: 674

PubMed: 21117060 Search on PubMed
DOI: https://doi.org/10.1002/prot.22916
Primary Citation of Related Structures:
2XSD

Organizational Affiliation

Laboratory of Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore. jauchr@gis.a-star.edu.sg

Macromolecule Content

Total Structure Weight: 25.22 kDa
Atom Count: 1,510
Modelled Residue Count: 150
Deposited Residue Count: 186
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
POU DOMAIN, CLASS 3, TRANSCRIPTION FACTOR 1	C	164	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P21952 (Mus musculus) Explore P21952 Go to UniProtKB: P21952
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21952
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(APTPGPCPAPTPGPAPGPGP*AP)-3'	A	11	N/A
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(CPCPTPCPAPTPGPCPAPTP*AP)-3'	B	11	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth C] MOL2 format, chain D [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C]	D [auth C], E [auth C], F [auth C], G [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Interactions & Density Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.232
R-Value Work: 0.194
R-Value Observed: 0.198
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.497	α = 90
b = 52.009	β = 129.03
c = 69.013	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-20
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description