4N9N | pdb_00004n9n

Crystal Structure of Saccharomyces cerevisiae Upc2 Transcription Factor fused with T4 Lysozyme

PDB DOI: https://doi.org/10.2210/pdb4N9N/pdb

Classification: TRANSCRIPTION
Organism(s): Saccharomyces cerevisiae S288C, Tequatrovirus T4
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-10-21 Released: 2014-12-03
Deposition Author(s): Yang, H., Im, Y.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.272 (Depositor), 0.268 (DCC)
R-Value Work:
0.251 (Depositor), 0.249 (DCC)
R-Value Observed:
0.251 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4N9N

This is version 1.2 of the entry. See complete history.

Literature

Structural mechanism of ergosterol regulation by fungal sterol nuclear receptor Upc2

Yang, H., Tong, J., Ha, S., Eom, S.H., Im, Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 99.71 kDa
Atom Count: 6,829
Modeled Residue Count: 856
Deposited Residue Count: 876
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sterol uptake control protein 2, Lysozyme	A, B	438	Saccharomyces cerevisiae S288C, Tequatrovirus T4	Mutation(s): 2 Gene Names: UPC2, E EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Find proteins for Q12151 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12151 Go to UniProtKB: Q12151
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P00720 Q12151
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.272 (Depositor), 0.268 (DCC)
R-Value Work: 0.251 (Depositor), 0.249 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.17	α = 90
b = 67.17	β = 90
c = 257.51	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 1.1: 2017-08-16
Changes: Refinement description, Source and taxonomy
Version 1.2: 2024-11-20
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.