2XSD | pdb_00002xsd

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 (Depositor), 0.229 (DCC)
R-Value Work:
0.194 (Depositor), 0.191 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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 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
Modeled Residue Count: 150
Deposited Residue Count: 186
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21952
Sequence Annotations Expand
Reference Sequence

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

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Molecule	Chains	Length	Organism
Entity ID: 2
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] mmCIF format, chain D [auth C] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF 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 (Depositor), 0.229 (DCC)
R-Value Work: 0.194 (Depositor), 0.191 (DCC)
R-Value Observed: 0.198 (Depositor)

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