3P5Q

Ferric R-state human aquomethemoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of human R-state aquomethemoglobin at 2.0 A resolution

Yi, J.Thomas, L.M.Richter-Addo, G.B.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 647-651

  • DOI: https://doi.org/10.1107/S1744309111012528
  • Primary Citation of Related Structures:  
    3P5Q

  • PubMed Abstract: 

    The crystal structure of tetrameric (αβ)(2) R-state human adult aquomethemoglobin is reported at 2.0 Å resolution. The asymmetric unit contained one αβ subunit pair. The R-state crystal belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 53.6, c = 192.8 Å. An Fe-bound water molecule was modeled into the heme distal pockets of each of the α and β subunits. In the α subunit, a highly ordered liganded water was modeled with an Fe-O(water) distance of 2.2 Å and appears to be protected against escape from the distal pocket by the conformation of the heme propionate groups, which point upwards towards the distal His58 residue aided by a hydrogen-bonding network involving the solvent. In the β subunit, the liganded water exhibited greater motion and was modeled with a longer Fe-O(water) distance of 2.5 Å; in this subunit both propionate groups point downwards away from the distal His63 residue, presumably allowing greater motion of the liganded water in and out of the distal pocket.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA. yijun@ou.edu


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta146Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
GTEx:  ENSG00000244734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.546α = 90
b = 53.546β = 90
c = 192.76γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-26
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description