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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1002/prot.22916
• Primary Citation of Related Structures:  
  2XSD

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Organizational Affiliation: 

Laboratory of Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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 ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*AP)-3'	A	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP)-3'	B	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth C], E [auth C], F [auth C], G [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (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

Entry History 

Deposition Data

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

Revision History  

• 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