4JCH | pdb_00004jch

OSH4 bound to an electrophilic oxysterol

PDB DOI: https://doi.org/10.2210/pdb4JCH/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2013-02-21 Released: 2014-03-26
Deposition Author(s): Koag, M.C., Kou, Y.I., Monzingo, A.F., Lee, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.215 (Depositor), 0.221 (DCC)
R-Value Work:
0.181 (Depositor), 0.189 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of OSH4 bound to an electrophilic oxysterol

Koag, M.C., Kou, Y., Monzingo, A.F., Lee, S.

To be published.

Macromolecule Content

Total Structure Weight: 100.49 kDa
Atom Count: 7,400
Modeled Residue Count: 866
Deposited Residue Count: 872
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein KES1	A, B	436	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: KES1, LPI3C, OSH4, P2614, YPL145C Membrane Entity: Yes
UniProt
Find proteins for P35844 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35844 Go to UniProtKB: P35844
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35844
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1KG Query on 1KG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	(3beta,9beta,22R,25R)-3-hydroxyfurost-5-en-27-yl propanoate C₃₀ H₄₈ O₄ LPEDPXMEGSUFII-ORSAPSQYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.215 (Depositor), 0.221 (DCC)
R-Value Work: 0.181 (Depositor), 0.189 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.62	α = 99.17
b = 65.689	β = 100.17
c = 77.939	γ = 96.76

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release
Version 1.1: 2015-01-07
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.