6UY1 | pdb_00006uy1

Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6UY1/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-09 Released: 2019-12-04 
• Deposition Author(s): Stavropoulos, P., Hoelz, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.228 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution

Stavropoulos, P., Hoelz, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Biological Assembly 8  

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

Biological assembly 8 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 109.99 kDa 
• Atom Count: 8,223 
• Modeled Residue Count: 881 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear protein STH1/NPS1	A, B, C, D, E, F, G, H	114	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: STH1, NPS1, YIL126W EC: 3.6.4.12
UniProt
Find proteins for P32597 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32597  Go to UniProtKB:  P32597

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	I [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.228 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.279	α = 90
b = 76.281	β = 96.65
c = 98.443	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-04 
Deposition Author(s): Stavropoulos, P., Hoelz, A.

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary