9RYG | pdb_00009ryg

Bifunctional Non-haem Iron Oxygenase NovR Involved in Novobiocin Biosynthesis with product bound

PDB DOI: https://doi.org/10.2210/pdb9RYG/pdb

Classification: LYASE
Organism(s): Streptomyces niveus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-15 Released: 2025-07-23
Deposition Author(s): Keller, S., Lawson, D.M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.188 (Depositor), 0.188 (DCC)
R-Value Work:
0.161 (Depositor), 0.161 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Bifunctional Non-haem Iron Oxygenase NovR Involved in Novobiocin Biosynthesis with product bound

Keller, S., Lawson, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 124.81 kDa
Atom Count: 9,253
Modeled Residue Count: 1,030
Deposited Residue Count: 1,100
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decarboxylase NovR	A, B, C, D	275	Streptomyces niveus	Mutation(s): 0 Gene Names: novR EC: 4.1
UniProt
Find proteins for Q9L9F0 (Streptomyces niveus) Explore Q9L9F0 Go to UniProtKB: Q9L9F0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9L9F0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JKI Query on A1JKI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	E [auth A], J [auth B], T [auth C], Z [auth D]	3-(3-methylbut-2-enyl)-4-oxidanyl-benzoic acid C₁₂ H₁₄ O₃ LBSJJNAMGVDGCU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain T [auth C] Focus chain Z [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain V [auth C]	BA [auth D] CA [auth D] G [auth A] L [auth B] M [auth B] BA [auth D], CA [auth D], G [auth A], L [auth B], M [auth B], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain V [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	DA [auth D] EA [auth D] FA [auth D] GA [auth D] H [auth A] DA [auth D], EA [auth D], FA [auth D], GA [auth D], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], W [auth C], X [auth C], Y [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain U [auth C]	AA [auth D], F [auth A], K [auth B], U [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain K [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain K [auth B] Focus chain U [auth C]