5I26 | pdb_00005i26

Azurin T30R1, crystal form I

• PDB DOI: https://doi.org/10.2210/pdb5I26/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-02-08 Released: 2016-04-13 
• Deposition Author(s): Hagelueken, G.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Determination of nitroxide spin label conformations via PELDOR and X-ray crystallography.

Abdullin, D., Hagelueken, G., Schiemann, O.

(2016) Phys Chem Chem Phys 18: 10428-10437

• PubMed: 27029516 
• DOI: https://doi.org/10.1039/c6cp01307d
• Primary Citation Related Structures: 
  5I26, 5I28


• PubMed Abstract: 
  

  Pulsed electron-electron double resonance (PELDOR or DEER) in combination with site-directed spin labelling has emerged as an important method for measuring nanometer distance constraints that are used to obtain coarse-grained structures of biomolecules or to follow their conformational changes. Translating measured spin-spin distances between spin labels into structural information requires taking the conformational flexibility of spin label side chains into account. Here, we present an analysis of orientation selective PELDOR data recorded on six singly MTSSL-labelled azurin mutants. The analysis yielded conformational MTSSL ensembles, which are considerably narrower than those predicted using in silico spin labeling methods but match well with spin label conformations found in the corresponding crystal structures. The possible reasons and consequences for predicting spin label conformers in the fold of biomolecules are discussed.

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Organizational Affiliation: 
• Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.85 kDa 
• Atom Count: 4,311 
• Modeled Residue Count: 508 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Azurin	A, B, C, D	128	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: azu, PA4922
UniProt
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

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
R1A	A, B, C, D	L-PEPTIDE LINKING	C12 H21 N2 O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.56	α = 90
b = 68.75	β = 96.75
c = 93.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Hagelueken, G.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	CRC 813, A6

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2016-04-20
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description