4Z67 | pdb_00004z67

The 1.5-angstrom crystal structure of Mn(2+)-bound PqqB from Pseudomonas Putida

• PDB DOI: https://doi.org/10.2210/pdb4Z67/pdb

• Classification: HORMONE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-03 Released: 2016-04-13 
• Deposition Author(s): Tu, X., Wilmot, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Crystal structures reveal metal-binding plasticity at the active site of PqqB

Tu, X., Wilmot, C.M.

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 (software)

Macromolecule Content 

• Total Structure Weight: 34.4 kDa 
• Atom Count: 2,817 
• Modeled Residue Count: 309 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme PQQ synthesis protein B	A	309	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: pqqB, PP_0379
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLT	C [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.327	α = 90
b = 86.327	β = 90
c = 107.064	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Tu, X., Wilmot, C.M.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations