8DLE

Crosslinked Crystal Structure of the 8-amino-7-oxonanoate synthase, BioF, and Benzene Sulfonyl Fluoride-crypto Acyl Carrier Protein, BSF-ACP

PDB DOI: https://doi.org/10.2210/pdb8DLE/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-07 Released: 2023-07-12
Deposition Author(s): Chen, A., Davis, T.D., Louie, G.V., Bowman, M.E., Noel, J.P., Burkart, M.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.246
R-Value Work: 0.203
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crosslinked Crystal Structure of the 8-amino-7-oxonanoate synthase, BioF, and Benzene Sulfonyl Fluoride-crypto Acyl Carrier Protein, BSF-ACP.

Chen, A., Davis, T.D., Re, R.N., Louie, G.V., Bowman, M.E., Tran, K., Clarke, D.J., MacKay, C.L., Campopiano, D.J., Noel, J.P., Burkart, M.D.

To be published.

Macromolecule Content

Total Structure Weight: 52.57 kDa
Atom Count: 3,700
Modelled Residue Count: 457
Deposited Residue Count: 470
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-amino-7-oxononanoate synthase	A	392	Escherichia coli	Mutation(s): 0 Gene Names: bioF, bioF_1, bioF_2 EC: 2.3.1.47
UniProt
Find proteins for P12998 (Escherichia coli (strain K12)) Explore P12998 Go to UniProtKB: P12998
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12998
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	B	78	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8 Go to UniProtKB: P0A6A8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6A8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SWC Query on SWC Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	N-{(2R)-2-hydroxy-3,3-dimethyl-4-[(trihydroxy-lambda~5~-phosphanyl)oxy]butanoyl}-beta-alanyl-N-(2-{4-[fluoro(dihydroxy)-lambda~4~-sulfanyl]phenyl}ethyl)-beta-alaninamide C₂₀ H₃₃ F N₃ O₁₀ P S AWRGUSCDENOWAW-SFHVURJKSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]