4IT8 | pdb_00004it8

A sperm whale myoglobin mutant L29H Mb with two distal histidines

• PDB DOI: https://doi.org/10.2210/pdb4IT8/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-01-18 Released: 2013-04-10 
• Deposition Author(s): Lin, Y.-W., Tan, X.-S., Li, W., Sun, M.-H., Wen, G.-B., Liu, J.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.187 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Structural and nitrite reductase activity comparisons of myoglobins with one to three distal histidines.

Sun, M.-H., Li, W., Liu, J.-H., Wen, G.-B., Tan, X.-S., Lin, Y.-W.

(2013) RSC Adv 

• DOI: https://doi.org/10.1039/C3RA40839F

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 18.01 kDa 
• Atom Count: 1,483 
• Modeled Residue Count: 153 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter macrocephalus	Mutation(s): 1  Gene Names: MB EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.187 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.899	α = 90
b = 48.433	β = 90
c = 78.923	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Lin, Y.-W., Tan, X.-S., Li, W., Sun, M.-H., Wen, G.-B., Liu, J.-H.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2013-06-05
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2026-03-04
  Changes: Refinement description, Structure summary