4S2Q | pdb_00004s2q

Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element

• PDB DOI: https://doi.org/10.2210/pdb4S2Q/pdb
• NAKB: 4S2Q

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


• Deposited: 2015-01-21 Released: 2016-02-17 
• Deposition Author(s): Vivekanandan, S., Moovarkumudalvan, B., Lescar, J., Kolatkar, P.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.269 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element

Vivekanandan, S., Moovarkumudalvan, B., Lescar, J., Kolatkar, P.R.

To be published.

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: 19.1 kDa 
• Atom Count: 1,314 
• Modeled Residue Count: 108 
• Deposited Residue Count: 108 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor SOX-9	C [auth D]	76	Mus musculus	Mutation(s): 0  Gene Names: Sox9, Sox-9
UniProt
Find proteins for Q04887 (Mus musculus) Explore Q04887  Go to UniProtKB:  Q04887

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*GP*CP*TP*TP*TP*GP*TP*TP*CP*TP*CP*CP*TP*G)-3')	A	16	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*GP*AP*GP*AP*AP*CP*AP*AP*AP*GP*CP*CP*TP*G)-3')	B	16	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.269 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.492	α = 90
b = 99.492	β = 90
c = 45.894	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Vivekanandan, S., Moovarkumudalvan, B., Lescar, J., Kolatkar, P.R.

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description