5SYD | pdb_00005syd

Circularly permutated azurin (cpAz) based on P. aeruginosa azurin sequence

• PDB DOI: https://doi.org/10.2210/pdb5SYD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa PAO1, Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-10 Released: 2017-08-16 
• Deposition Author(s): Petrik, I., Yang, Y., Howard, R., Yi, L.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Circular Permutation of Azurin Results in the same Type 1 Blue Copper with different Reduction Potentials

Yu, Y., Petrik, I., Chacon, K.N., Hosseinzadeh, P., Blackburn, N., Yi, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.41 kDa 
• Atom Count: 2,089 
• Modeled Residue Count: 261 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Azurin, chimeric construct	A, B	131	Pseudomonas aeruginosa PAO1, Pseudomonas aeruginosa This entity is chimeric	Mutation(s): 0  Gene Names: azu, PA4922
UniProt
Find proteins for B3EWN9 (Pseudomonas aeruginosa) Explore B3EWN9  Go to UniProtKB:  B3EWN9
Find proteins for P00282 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P00282  Go to UniProtKB:  P00282
UniProt Groups	B3EWN9P00282

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	C [auth A], D [auth A], E [auth A], F [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.436	α = 90
b = 115.436	β = 90
c = 83.145	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
Coot	model building
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Petrik, I., Yang, Y., Howard, R., Yi, L.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary