2Z68

Crystal Structure Of An Artificial Metalloprotein: Cr[N-salicylidene-4-amino-3-hydroxyhydrocinnamic acid]/Wild Type Heme oxygenase

• PDB DOI: https://doi.org/10.2210/pdb2Z68/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-07-24 Released: 2007-08-28 
• Deposition Author(s): Yokoi, N., Unno, M., Ueno, T., Ikeda-Saito, M., Watanabe, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.225 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Ligand design for the improvement of stability of metal complex.protein hybrids.

Yokoi, N., Ueno, T., Unno, M., Matsui, T., Ikeda-Saito, M., Watanabe, Y.

(2008) Chem Commun (Camb) : 229-231

• PubMed: 18092096 
• DOI: https://doi.org/10.1039/b713468a
• Primary Citation of Related Structures:  
  2Z68


• PubMed Abstract: 
  

  We have succeeded in improving the stability of Fe(Schiff-base).heme oxygenase (HO) hybrids by ligand design based on the crystal structure of Fe(N,N'-bis(salicylidene)-3.4-diaminobenzene propionic acid).HO.

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Organizational Affiliation: 

Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.

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: 49.35 kDa 
• Atom Count: 3,802 
• Modelled Residue Count: 417 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme oxygenase	A, B	215	Corynebacterium diphtheriae	Mutation(s): 0  EC: 1.14.99.3
UniProt
Find proteins for Q54AI1 (Corynebacterium diphtheriae) Explore Q54AI1  Go to UniProtKB:  Q54AI1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TIL	F [auth A], I [auth B]	[2-[5-CARBOXYETHYL-2-PHENOLATO(NITRILOMETHYLIDYNE)][PHENOLATO]]CHROMIUM(III) C16 H13 Cr N O4 PQEURDOLYHRQIK-LZMXEPDESA-L
SO4	C [auth A], D [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	E [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.225 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.656	α = 90
b = 63.057	β = 96.88
c = 77.964	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-28 
Deposition Author(s): Yokoi, N., Unno, M., Ueno, T., Ikeda-Saito, M., Watanabe, Y.

Revision History  

• Version 1.0: 2007-08-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-09-18
  Changes: Database references