3G2B

crystal structure of PqqD from xanthomonas campestris

• PDB DOI: https://doi.org/10.2210/pdb3G2B/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Xanthomonas campestris pv. campestris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-31 Released: 2009-09-01 
• Deposition Author(s): Yang, C.-Y., Tsai, T.-Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.228 
• R-Value Work: 0.196 

Literature

Xanthomonas campestris PqqD in the pyrroloquinoline quinone biosynthesis operon adopts a novel saddle-like fold that possibly serves as a PQQ carrier

Tsai, T.-Y., Yang, C.-Y., Shih, H.-L., Wang, A.H.-J., Chou, S.-H.

(2009) Proteins 76: 1042-1048

• PubMed: 19475705 
• DOI: https://doi.org/10.1002/prot.22461
• Primary Citation of Related Structures:  
  3G2B

---

Organizational Affiliation: 

Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227, Taiwan, Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 10.68 kDa 
• Atom Count: 817 
• Modelled Residue Count: 90 
• Deposited Residue Count: 95 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme PQQ synthesis protein D	A	95	Xanthomonas campestris pv. campestris	Mutation(s): 0  Gene Names: pqqD
UniProt
Find proteins for Q8P6M8 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P6M8  Go to UniProtKB:  Q8P6M8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.228 
• R-Value Work: 0.196 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.9	α = 90
b = 66.25	β = 90
c = 93.88	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Yang, C.-Y., Tsai, T.-Y.

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations