3AY2 | pdb_00003ay2

Crystal structure of Neisserial azurin

• PDB DOI: https://doi.org/10.2210/pdb3AY2/pdb

• Classification: ANTITUMOR PROTEIN, ANTIVIRAL PROTEIN
• Organism(s): Neisseria gonorrhoeae FA 1090
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-04-24 Released: 2012-05-02 
• Deposition Author(s): Ochiai, A., Hashimoto, W., Yamada, T., Chakrabarty, A.M., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Neisserial Azurin

Hashimoto, W., Ochiai, A., Yamada, T., Chakrabarty, A.M., Murata, K.

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: 34.49 kDa 
• Atom Count: 2,215 
• Modeled Residue Count: 252 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid modified azurin protein	A, B	167	Neisseria gonorrhoeae FA 1090	Mutation(s): 2  Gene Names: NGO0994
UniProt
Find proteins for Q5F809 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F809  Go to UniProtKB:  Q5F809

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.513	α = 90
b = 77.513	β = 90
c = 94.577	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Ochiai, A., Hashimoto, W., Yamada, T., Chakrabarty, A.M., Murata, K.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary