2W6Y | pdb_00002w6y

Crystal structure of Sperm Whale Myoglobin mutant YQR in complex with Xenon

• PDB DOI: https://doi.org/10.2210/pdb2W6Y/pdb

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


• Deposited: 2008-12-19 Released: 2009-12-22 
• Deposition Author(s): Miele, A.E., Draghi, F., Renzi, F., Sciara, G., Johnson, K.A., Vallone, B., Brunori, M., Savino, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.196 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.186 (DCC) 

Starting Model: experimental

Literature

When the Same Fold Does not Mean the Same Function: The Case of Xenon Cavities in Hemoglobin and Myoglobin

Miele, A.E., Draghi, F., Johnson, K.A., Renzi, F., Sciara, G., Brunori, M., Vallone, B., Savino, C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 18.89 kDa 
• Atom Count: 1,572 
• 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): 3  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	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
XE	F [auth A], G [auth A], H [auth A], I [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.196 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.186 (DCC) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.626	α = 90
b = 90.626	β = 90
c = 45.505	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Miele, A.E., Draghi, F., Renzi, F., Sciara, G., Johnson, K.A., Vallone, B., Brunori, M., Savino, C.

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description