2Z6S | pdb_00002z6s

Crystal structure of the oxy myoglobin free from X-ray-induced photoreduction

• PDB DOI: https://doi.org/10.2210/pdb2Z6S/pdb

• Classification: OXYGEN BINDING
• Organism(s): Physeter macrocephalus
• Mutation(s): No 


• Deposited: 2007-08-08 Released: 2007-11-06 
• Deposition Author(s): Unno, M., Kusama, S., Chen, H., Shaik, S., Ikeda-Saito, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.187 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of the Fleeting Ferric Peroxo Species in Myoglobin: Experiment and Theory

Unno, M., Chen, H., Kusama, S., Shaik, S., Ikeda-Saito, M.

(2007) J Am Chem Soc 129: 13394-13395

• PubMed: 17929929 
• DOI: https://doi.org/10.1021/ja076108x
• Primary Citation Related Structures: 
  2Z6S, 2Z6T

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Organizational Affiliation: 
• Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan.

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: 18.08 kDa 
• Atom Count: 1,529 
• Modeled Residue Count: 152 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Physeter macrocephalus	Mutation(s): 0  EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
OXY	E [auth A]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.187 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.338	α = 90
b = 30.699	β = 105.46
c = 63.674	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Unno, M., Kusama, S., Chen, H., Shaik, S., Ikeda-Saito, M.

Revision History  

• Version 1.0: 2007-11-06
  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