2HMZ | pdb_00002hmz

THE STRUCTURES OF MET AND AZIDOMET HEMERYTHRIN AT 1.66 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2HMZ/pdb
• Entry: 2HMZ supersedes: 1HMZ

• Classification: OXYGEN TRANSPORT
• Organism(s): Themiste dyscritum
• Mutation(s): Yes 


• Deposited: 1990-10-18 Released: 1992-01-15 
• Deposition Author(s): Holmes, M.A., Stenkamp, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Work: 
  0.162 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Structures of met and azidomet hemerythrin at 1.66 A resolution.

Holmes, M.A., Stenkamp, R.E.

(1991) J Mol Biology 220: 723-737

• PubMed: 1870128 
• DOI: https://doi.org/10.1016/0022-2836(91)90113-k
• Primary Citation Related Structures: 
  2HMQ, 2HMZ


• PubMed Abstract: 
  

  The crystallographic refinement of met and azidomet hemerythrin has been carried out at 1.66 A resolution in an attempt to characterize precisely the binuclear iron center in this protein. Restrained least-squares refinement has produced molecular models giving R-values of 18.9% for met (65,683 reflections from 10 A to 1.66 A) and 17.6% for azidomet hemerythrin (68,747 reflections from 10.0 A to 1.66 A). The protein structure in each derivative is very similar to that of myohemerythrin. The mu-oxo bridged iron center differs between the two forms. The complex in met hemerythrin is asymmetric with the bridging oxygen closer to one of the iron atoms while the complex in azidomet hemerythrin is symmetric. After investigations of the effects of correlation in the refinement, we believe this difference between the two complexes is associated with chemical differences and is not a refinement artefact.

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Organizational Affiliation: 
• Department of Biological Structure, University of Washington, Seattle 98195.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 54.33 kDa 
• Atom Count: 4,151 
• Modeled Residue Count: 456 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMERYTHRIN	A, B, C, D	113	Themiste dyscritum	Mutation(s): 1
UniProt
Find proteins for P02246 (Themiste dyscrita) Explore P02246  Go to UniProtKB:  P02246

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FEA	F [auth A], H [auth B], J [auth C], L [auth D]	MONOAZIDO-MU-OXO-DIIRON Fe2 N3 O GTUZFHRZTDZJHZ-UHFFFAOYSA-N
ACT	E [auth A], G [auth B], I [auth C], K [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Work:  0.162 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.6	α = 90
b = 86.6	β = 90
c = 80.8	γ = 90

Software Package:

Software Name	Purpose
PROFFT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-01-15 
Deposition Author(s): Holmes, M.A., Stenkamp, R.E.
• This entry supersedes: 1HMZ

Revision History  

• Version 1.0: 1992-01-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other