1J52 | pdb_00001j52

Recombinant sperm whale myoglobin in the presence of 7atm xenon

• PDB DOI: https://doi.org/10.2210/pdb1J52/pdb

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


• Deposited: 2002-01-08 Released: 2003-11-11 
• Deposition Author(s): Liong, E.C., Phillips Jr., G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.205 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.157 (DCC) 

Starting Model: experimental

Literature

Internal Cavities in Myoglobin: Implications for Protein Action

Radding, W., Liong, E.C., Phillips Jr., G.N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.6 kDa 
• Atom Count: 1,420 
• Modeled Residue Count: 154 
• 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  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	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
XE	D [auth A], E [auth A], F [auth A], G [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.205 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.157 (DCC) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.58	α = 90
b = 91.58	β = 90
c = 45.97	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
XDS	data reduction
X-PLOR	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-11 
Deposition Author(s): Liong, E.C., Phillips Jr., G.N.

Revision History  

• Version 1.0: 2003-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-16
  Changes: Data collection, Refinement description