4YX6 | pdb_00004yx6

Architectural hierarchy of trans-acting enoyl reductases from polyunsaturated fatty acid and trans-AT polyketide synthases

PDB DOI: https://doi.org/10.2210/pdb4YX6/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Shewanella oneidensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-03-22 Released: 2016-04-13
Deposition Author(s): Till, M., Race, P.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.199 (Depositor), 0.209 (DCC)
R-Value Work:
0.173 (Depositor), 0.187 (DCC)
R-Value Observed:
0.175 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Architectural hierarchy of trans-acting enoyl reductases from polyunsaturated fatty acid and trans-AT polyketide synthases

Till, M., Race, P.R.

To be published.

Macromolecule Content

Total Structure Weight: 120.33 kDa
Atom Count: 8,098
Modeled Residue Count: 1,020
Deposited Residue Count: 1,094
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Omega-3 polyunsaturated fatty acid synthase subunit PfaD	A, B	547	Shewanella oneidensis	Mutation(s): 0 Gene Names: pfaD, SO_1597
UniProt
Find proteins for Q8EGK4 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EGK4 Go to UniProtKB: Q8EGK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8EGK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.199 (Depositor), 0.209 (DCC)
R-Value Work: 0.173 (Depositor), 0.187 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.57	α = 90
b = 105.57	β = 90
c = 214.55	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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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.