6N04 | pdb_00006n04

The X-ray crystal structure of AbsH3, an FAD dependent reductase from the Abyssomicin biosynthesis pathway in Streptomyces

PDB DOI: https://doi.org/10.2210/pdb6N04/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces sp. LC-6-2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-11-06 Released: 2019-11-13
Deposition Author(s): Clinger, J.A., Wang, X., Cai, W., Miller, M.D., Van Lanen, S.G., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.236 (Depositor), 0.238 (DCC)
R-Value Work:
0.183 (Depositor), 0.185 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

The crystal structure of AbsH3: A putative flavin adenine dinucleotide-dependent reductase in the abyssomicin biosynthesis pathway.

Clinger, J.A., Wang, X., Cai, W., Zhu, Y., Miller, M.D., Zhan, C.G., Van Lanen, S.G., Thorson, J.S., Phillips Jr., G.N.

(2020) Proteins

PubMed: 32852843 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.25994
Primary Citation Related Structures:
6N04

PubMed Abstract:
Natural products and natural product-derived compounds have been widely used for pharmaceuticals for many years, and the search for new natural products that may have interesting activity is ongoing. Abyssomicins are natural product molecules that have antibiotic activity via inhibition of the folate synthesis pathway in microbiota. These compounds also appear to undergo a required [4 + 2] cycloaddition in their biosynthetic pathway. Here we report the structure of an flavin adenine dinucleotide-dependent reductase, AbsH3, from the biosynthetic gene cluster of novel abyssomicins found in Streptomyces sp. LC-6-2.

Organizational Affiliation

Department of Biosciences, Rice University, Houston, Texas, USA.

Macromolecule Content

Total Structure Weight: 93.82 kDa
Atom Count: 6,559
Modeled Residue Count: 731
Deposited Residue Count: 868
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AbsH3	A, B	434	Streptomyces sp. LC-6-2	Mutation(s): 0 EC: 1.14.13
UniProt
Find proteins for A0A1V0QH64 (Streptomyces sp. LC-6-2) Explore A0A1V0QH64 Go to UniProtKB: A0A1V0QH64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1V0QH64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		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: 2.00 Å
R-Value Free: 0.236 (Depositor), 0.238 (DCC)
R-Value Work: 0.183 (Depositor), 0.185 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.316	α = 90
b = 109.491	β = 90
c = 143.637	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 CA217255-01A1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM115261-02