1XTO | pdb_00001xto

Crystal Structure of the Coenzyme PQQ Synthesis Protein (PqqB) from Pseudomonas putida, Northeast Structural Genomics Target PpR6

• PDB DOI: https://doi.org/10.2210/pdb1XTO/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-10-22 Released: 2004-11-09 
• Deposition Author(s): Forouhar, F., Chen, Y., Kuzin, A., Vorobiev, S.M., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal Structure of the Coenzyme PQQ Synthesis Protein (PqqB) from Pseudomonas putida, Northeast Structural Genomics Target PpR6

Forouhar, F., Chen, Y., Kuzin, A., Vorobiev, S.M., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 35.02 kDa 
• Atom Count: 2,378 
• Modelled Residue Count: 304 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme PQQ synthesis protein B	A	311	Pseudomonas putida KT2440	Mutation(s): 11  Gene Names: pqqB
UniProt
Find proteins for Q88QV5 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88QV5  Go to UniProtKB:  Q88QV5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.051	α = 90
b = 86.051	β = 90
c = 110.666	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-09 
Deposition Author(s): Forouhar, F., Chen, Y., Kuzin, A., Vorobiev, S.M., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2004-11-09
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-09
  Changes: Structure summary