7R7E

Synechococcus Olefin Synthase FAAL domain in complex with AMP and pyrophosphate

PDB DOI: https://doi.org/10.2210/pdb7R7E/pdb

Classification: LIGASE
Organism(s): Picosynechococcus sp. PCC 7002
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-06-24 Released: 2022-07-06
Deposition Author(s): Sikkema, A.P., Strugis, R.M., Smith, J.L.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.239
R-Value Work: 0.196
R-Value Observed: 0.198

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

An electrostatic fatty acid selection mechanism by the Olefin Synthase FAAL domain from Synechococcus sp. PCC7002

Sikkema, A.P., Sturgis, R.M., Gerwick, W.H., Sherman, D.H., Smith, J.L.

To be published.

Macromolecule Content

Total Structure Weight: 125.2 kDa
Atom Count: 9,384
Modelled Residue Count: 1,134
Deposited Residue Count: 1,144
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase	A, B	572	Picosynechococcus sp. PCC 7002	Mutation(s): 0 Gene Names: SYNPCC7002_A1173 EC: 6.2.1.20
UniProt
Find proteins for B1XKC6 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6)) Explore B1XKC6 Go to UniProtKB: B1XKC6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1XKC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
POP (Subject of Investigation/LOI) Query on POP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.239
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.288	α = 90
b = 60.92	β = 101.175
c = 95.929	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Sikkema, A.P.

Strugis, R.M.

Smith, J.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK042303
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA108874
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118101
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM008270
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	AGM-12006
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	ACB-12002
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM138396