9S2T | pdb_00009s2t

Carbamoyl transferase NovN involved in Novobiocin biosynthesis

PDB DOI: https://doi.org/10.2210/pdb9S2T/pdb

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

Deposited: 2025-07-22 Released: 2025-07-30
Deposition Author(s): Gomez Garcia, I., Lawson, D.M.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.160 (Depositor), 0.160 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 9S2T

Ligand Structure Quality Assessment

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

Literature

Carbamoyl transferase NovN involved in Novobiocin biosynthesis

Gomez Garcia, I., Lawson, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 76.4 kDa
Atom Count: 5,747
Modeled Residue Count: 669
Deposited Residue Count: 687
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decarbamoylnovobiocin carbamoyltransferase	A	687	Streptomyces niveus	Mutation(s): 0 Gene Names: novN EC: 2.1.3.12
UniProt
Find proteins for Q9L9F4 (Streptomyces niveus) Explore Q9L9F4 Go to UniProtKB: Q9L9F4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9L9F4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], H [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.160 (Depositor), 0.160 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.5	α = 90
b = 113.26	β = 90
c = 166.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOSFLM	data reduction
gemmi	data extraction
SHELXDE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Gomez Garcia, I.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	B19400

Revision History (Full details and data files)

Version 1.0: 2025-07-30
Type: Initial release

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