3RGK | pdb_00003rgk

Crystal Structure of Human Myoglobin Mutant K45R

• PDB DOI: https://doi.org/10.2210/pdb3RGK/pdb
• Entry: 3RGK supersedes: 2MM1

• Classification: OXYGEN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-04-08 Released: 2011-04-27 
• Deposition Author(s): Hubbard, S.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of a recombinant human myoglobin mutant at 2.8 A resolution

Hubbard, S.R., Lambright, S.G., Boxer, S.G., Hendrickson, W.A.

(1990) J Mol Biology 20: 215-218

• PubMed: 2342104 
• DOI: https://doi.org/10.1016/S0022-2836(05)80181-0
• Primary Citation Related Structures: 
  3RGK


• PubMed Abstract: 
  

  We have grown crystals in trigonal space group P3(2)21 of a mutant human myoglobin, aquomet form, in which lysine at position 45 has been replaced by arginine and cysteine at position 110 has been replaced by alanine. Suitable crystals of native recombinant human myoglobin have not been obtained. We have used the molecular replacement method to determine the X-ray crystal structure of the mutant at 2.8 A resolution. At the present stage of refinement, the crystallographic R-value for the model, with tightly restrained stereochemistry, is 0.158 for 5.0 to 2.8 A data. As expected, the overall structure is quite similar to the sperm whale myoglobin structure. Arginine 45 adopts a well-ordered conformation similar to that found in aquomet sperm whale myoglobin.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.

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: 17.98 kDa 
• Atom Count: 1,347 
• Modeled Residue Count: 149 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Homo sapiens	Mutation(s): 2  Gene Names: MB EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P02144 (Homo sapiens) Explore P02144  Go to UniProtKB:  P02144
PHAROS:  P02144 GTEx:  ENSG00000198125

Small Molecules

Ligands 2 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
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: 1.65 Å
• R-Value Free:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.2	α = 90
b = 86.2	β = 90
c = 35.66	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Hubbard, S.R.
• This entry supersedes: 2MM1

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description