1A4B

AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 6.5 CRYSTAL FORM, DATA COLLECTED AT-180 DEGREES CELSIUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Rack-induced metal binding vs. flexibility: Met121His azurin crystal structures at different pH.

Messerschmidt, A.Prade, L.Kroes, S.J.Sanders-Loehr, J.Huber, R.Canters, G.W.

(1998) Proc.Natl.Acad.Sci.USA 95: 3443-3448

  • Primary Citation of Related Structures:  1A4A, 1A4C

  • PubMed Abstract: 
  • The rack-induced bonding mechanism of metals to proteins is a useful concept for explaining the generation of metal sites in electron transfer proteins, such as the blue copper proteins, that are designed for rapid electron transfer. The trigonal pyr ...

    The rack-induced bonding mechanism of metals to proteins is a useful concept for explaining the generation of metal sites in electron transfer proteins, such as the blue copper proteins, that are designed for rapid electron transfer. The trigonal pyramidal structure imposed by the protein with three strong equatorial ligands (one Cys and two His) provides a favorable geometry for both cuprous and cupric oxidation states. However, the crystal structures of the Met121His mutant of azurin from Alcaligenes denitrificans at pH 6.5 (1.89- and 1.91-A resolutions) and pH 3.5 (2.45-A resolution) show that the preformed metal binding cavity in the protein is more flexible than expected. At high pH (6.5), the Cu site retains the same three equatorial ligands as in the wild-type azurin and adds His121 as a fourth strong ligand, creating a tetrahedral copper site geometry with a green color referred to as 1.5 type. In the low pH (3.5) structure, the protonation of His121 causes a conformational change in residues 117-123, moving His121 away from the copper. The empty coordination site is occupied by an oxygen atom of a nitrate molecule of the buffer solution. This axial ligand is coordinated less strongly, generating a distorted tetrahedral copper geometry with a blue color and spectroscopic properties of a type-1 site. These crystal structures demonstrate that blue copper proteins are flexible enough to permit a range of movement of the Cu atom along the axial direction of the trigonal pyramid.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany. messersc@biochem.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AZURIN
A, B
129Achromobacter denitrificansGene Names: azu
Find proteins for P00280 (Achromobacter denitrificans)
Go to UniProtKB:  P00280
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Work: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 74.560α = 90.00
b = 73.570β = 90.00
c = 97.630γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
AMoREphasing
ROTAVATAdata reduction
Agrovatadata reduction
X-PLORrefinement
ROTAVATAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Refinement description