4Z7R

The 1.98-angstrom crystal structure of Zn(2+)-bound PqqB from Methylobacterium extorquens

• PDB DOI: https://doi.org/10.2210/pdb4Z7R/pdb

• Classification: HYDROLASE
• Organism(s): Methylorubrum extorquens AM1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-07 Released: 2016-04-20 
• Deposition Author(s): Tu, X., Wilmot, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.221 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

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

Tu, X., Wimot, 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: 64.66 kDa 
• Atom Count: 4,602 
• Modelled Residue Count: 578 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme PQQ synthesis protein B	A, B	299	Methylorubrum extorquens AM1	Mutation(s): 0  Gene Names: pqqB, pqqG, MexAM1_META1p1750
UniProt
Find proteins for Q49149 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore Q49149  Go to UniProtKB:  Q49149

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.221 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.431	α = 90
b = 51.991	β = 95.49
c = 120.536	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Tu, X., Wilmot, C.M.

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations