6YSV | pdb_00006ysv

E. coli anaerobic trifunctional enzyme subunit-alpha

PDB DOI: https://doi.org/10.2210/pdb6YSV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-23 Released: 2021-05-12
Deposition Author(s): Sah-Teli, S.K., Hynonen, M.J., Wierenga, R.K., Venkatesan, R.
Funding Organization(s): Academy of Finland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.255 (Depositor), 0.257 (DCC)
R-Value Work:
0.224 (Depositor), 0.228 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6YSV

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

Literature

Structural basis for different membrane-binding properties of E. coli anaerobic and human mitochondrial beta-oxidation trifunctional enzymes

Sah-Teli, S.K., Pinkas, M., Hynonen, M.J., Butcher, S.J., Wierenga, R.K., Novacek, J., Venkatesan, R.

(2023) Structure

DOI: https://doi.org/10.1016/j.str.2023.04.011

Macromolecule Content

Total Structure Weight: 158.25 kDa
Atom Count: 10,549
Modeled Residue Count: 1,407
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid oxidation complex subunit alpha	A, B	728	Escherichia coli K-12	Mutation(s): 0 Gene Names: fadJ, yfcX, b2341, JW2338 EC: 4.2.1.17 (PDB Primary Data), 5.1.2.3 (PDB Primary Data), 1.1.1.35 (PDB Primary Data)
UniProt
Find proteins for P77399 (Escherichia coli (strain K12)) Explore P77399 Go to UniProtKB: P77399
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77399
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.255 (Depositor), 0.257 (DCC)
R-Value Work: 0.224 (Depositor), 0.228 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.583	α = 90
b = 90.751	β = 96.112
c = 172.912	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MoRDa	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Academy of Finland	Finland	289024, 293369, 319194

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2023-05-17
Changes: Database references
Version 1.2: 2024-02-07
Changes: Data collection, 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.