6II1 | pdb_00006ii1

Crystal Structure Analysis of CO form hemoglobin from Bos taurus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 
    0.175 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 
    0.138 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Quaternary Structure Analysis of a Hemoglobin Core in Hemoglobin-Albumin Cluster.

Morita, Y.Yamada, T.Kureishi, M.Kihira, K.Komatsu, T.

(2018) J Phys Chem B 122: 12031-12039

  • DOI: https://doi.org/10.1021/acs.jpcb.8b10077
  • Primary Citation Related Structures: 
    6IHX, 6II1

  • PubMed Abstract: 

    A core-shell ensemble of bovine hemoglobin (Hb) and human serum albumin (HSA) is an artificial O 2 carrier as a red blood cell substitute. This protein particle is created by covalent wrapping of a carbonyl Hb with HSAs: Hb R -HSA 3 cluster, where Hb R signifies the use of carbonyl Hb (relaxed (R) state conformation) as a starting material. The Hb R -HSA 3 cluster exhibits high O 2 affinity and low cooperativity. Analysis of the quaternary structure of the central Hb R in the cluster revealed that its high O 2 affinity is attributed to the physically immobile Hb R nucleus. Circular dichroism and UV-vis absorption spectroscopy showed that the structure of deoxy Hb R core closely resembles the R-state. The crystal structure of Lys-modified carbonyl Hb R was superimposed on that of carbonyl Hb. These results imply that chemical modifications of the surface Lys groups and Cys-93(β) of the carbonyl Hb with cross-linking agent interfered in the quaternary structure movement from the R-state to tense (T) state. As expected, coupling of deoxy Hb (T-state) with HSAs yielded Hb T -HSA 3 cluster having low O 2 affinity. The mixing of Hb R -HSA 3 and Hb T -HSA 3 clusters conferred a tailor-made formulation of artificial O 2 carrier with a desired O 2 affinity ( P 50 ).


  • Organizational Affiliation
    • Department of Applied Chemistry, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan.

Macromolecule Content 

  • Total Structure Weight: 63.79 kDa 
  • Atom Count: 5,230 
  • Modeled Residue Count: 563 
  • Deposited Residue Count: 566 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha
A, C
138Bos taurusMutation(s): 0 
UniProt
Find proteins for P01966 (Bos taurus)
Explore P01966 
Go to UniProtKB:  P01966
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01966
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta
B, D
145Bos taurusMutation(s): 0 
UniProt
Find proteins for P02070 (Bos taurus)
Explore P02070 
Go to UniProtKB:  P02070
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02070
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CMO

Query on CMO



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free:  0.175 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 0.138 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.56α = 90
b = 76.283β = 90
c = 109.789γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description