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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.228 (Depositor), 0.240 (DCC)
R-Value Work:
0.184 (Depositor), 0.200 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6UY1

This is version 1.1 of the entry. See complete history.

Literature

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

Stavropoulos, P., Hoelz, A.

To be published.

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

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear protein STH1/NPS1	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32597
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth E] MOL2 format, chain I [auth E] mmCIF format, chain I [auth E]	I [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth E] Interactions & Density Focus chain I [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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), 0.240 (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

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Entry History

Deposition Data

Released Date: 2019-12-04

Deposition Author(s):

Stavropoulos, P.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.