4Z9R | pdb_00004z9r

Crystal structure of PfaD from Shewanella oneidensis in complex with NAD+ determined by in-situ diffraction.

PDB DOI: https://doi.org/10.2210/pdb4Z9R/pdb

Classification: OXIDOREDUCTASE
Organism(s): Shewanella oneidensis MR-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-11 Released: 2016-04-06
Deposition Author(s): Baker, G.E., Race, P.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.253 (Depositor), 0.250 (DCC)
R-Value Work:
0.212 (Depositor), 0.214 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of PfaD from Shewanella oneidensis in complex with NAD+ determined by in-situ diffraction.

Baker, G.E., Race, P.R.

To be published.

Macromolecule Content

Total Structure Weight: 121.58 kDa
Atom Count: 7,525
Modeled Residue Count: 996
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 MR-1	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
NAD Query on NAD 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]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-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: 2.80 Å
R-Value Free: 0.253 (Depositor), 0.250 (DCC)
R-Value Work: 0.212 (Depositor), 0.214 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.68	α = 90
b = 106.68	β = 90
c = 217.477	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Coot	model building
XDS	data reduction
Aimless	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-04-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-06
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, 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.