9ZNJ | pdb_00009znj

Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 6,7-dimethyl-8-(1'-D-ribityl) lumazine

PDB DOI: https://doi.org/10.2210/pdb9ZNJ/pdb

Classification: TRANSFERASE
Organism(s): Bordetella pertussis Tohama I
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-12-12 Released: 2025-12-24
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.261 (Depositor), 0.261 (DCC)
R-Value Work:
0.224 (Depositor), 0.225 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of 6,7-dimethyl-8-ribityllumazine synthase from Bordetella pertussis in complex with 6,7-dimethyl-8-(1'-D-ribityl) lumazine

Seibold, S., Lovell, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 89.36 kDa
Atom Count: 5,624
Modeled Residue Count: 763
Deposited Residue Count: 815
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A, B, C, D, E	163	Bordetella pertussis Tohama I	Mutation(s): 0 Gene Names: ribH, BP3485 EC: 2.5.1.78
UniProt
Find proteins for Q7VTN4 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VTN4 Go to UniProtKB: Q7VTN4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7VTN4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DLZ (Subject of Investigation/LOI) Query on DLZ Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain FA [auth E] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C]	AA [auth D], FA [auth E], L [auth A], Q [auth B], W [auth C]	1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol C₁₃ H₁₈ N₄ O₆ SXDXRJZUAJBNFL-XKSSXDPKSA-N		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain L [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain L [auth A] Focus chain Q [auth B] Focus chain W [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] SDF format, chain CA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] MOL2 format, chain CA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D] mmCIF format, chain CA [auth E]	BA [auth E] CA [auth E] F [auth A] M [auth B] R [auth C] BA [auth E], CA [auth E], F [auth A], M [auth B], R [auth C], X [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain F [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain F [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain K [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain K [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain K [auth A]	DA [auth E] EA [auth E] G [auth A] H [auth A] I [auth A] DA [auth E], EA [auth E], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C], V [auth C], Y [auth D], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth E] Focus chain EA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain EA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.261 (Depositor), 0.261 (DCC)
R-Value Work: 0.224 (Depositor), 0.225 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.448	α = 90
b = 75.416	β = 114.38
c = 94.461	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394