7DIH | pdb_00007dih

Crystal structure of Thermoglobin Y29F mutant in complex with imidazole

• PDB DOI: https://doi.org/10.2210/pdb7DIH/pdb

• Classification: OXYGEN BINDING
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-11-19 Released: 2021-01-20 
• Deposition Author(s): Muraki, N., Aono, S.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of Y29F Mutant of Thermoglobin from a Hyperthermophilic Bacterium Aquifex aeolicus

Muraki, N., Takeda, K., Nam, D., Muraki, M., Aono, S.

(2021) Chem Lett 

• DOI: https://doi.org/10.1246/cl.200879

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration, homology

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: 33.97 kDa 
• Atom Count: 2,398 
• Modeled Residue Count: 276 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermoglobin	A, B	142	Aquifex aeolicus VF5	Mutation(s): 1  Gene Names: aq_211
UniProt
Find proteins for O66586 (Aquifex aeolicus (strain VF5)) Explore O66586  Go to UniProtKB:  O66586

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
IMD (Subject of Investigation/LOI)	D [auth A], G [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.771	α = 90
b = 35.823	β = 95.2
c = 138.084	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
BUCCANEER	model building
MOLREP	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Muraki, N., Aono, S.

---

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H05762

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description