6B8S

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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.239 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Literature

Crystal Structure of Dihydroorotate Dehydrogenase from Helicobacter pylori with bound FMN

Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

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 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M36B8S

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