6B8S | pdb_00006b8s

Crystal Structure of Dihydroorotate Dehydrogenase from Helicobacter pylori with bound FMN

• PDB DOI: https://doi.org/10.2210/pdb6B8S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori G27
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2017-10-09 Released: 2017-11-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of di­hydroorotate de­hydrogenase from Helicobacter pylori with bound flavin mononucleotide

Agarwal, A.A., Georgiades, J.D., Dranow, D.M., Lorimer, D.D., Edwards, T.E., Barrett, K.F., Craig, J.K., Van Voorhis, W.C., Myler, P.J., Smith, C.L.

(2025) Acta Crystallogr F Struct Biol Commun 81: 108-117

• DOI: https://doi.org/10.1107/S2053230X25000858

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.34 kDa 
• Atom Count: 5,161 
• Modelled Residue Count: 671 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone)	A, B	359	Helicobacter pylori G27	Mutation(s): 0  Gene Names: pyrD, HPG27_417 EC: 1.3.5.2 Membrane Entity: Yes
UniProt
Find proteins for B5Z6I2 (Helicobacter pylori (strain G27)) Explore B5Z6I2  Go to UniProtKB:  B5Z6I2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PGE	D [auth A], F [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36B8S

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.44	α = 90
b = 69.08	β = 98.06
c = 100.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Data collection
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2025-03-05
  Changes: Database references, Structure summary