2DXM

Neutron Structure Analysis of Deoxy Human Hemoglobin

• PDB DOI: https://doi.org/10.2210/pdb2DXM/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-28 Released: 2007-12-04 
• Deposition Author(s): Morimoto, Y.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.260 
• R-Value Work: 0.197 

Literature

Protonation states of buried histidine residues in human deoxyhemoglobin revealed by neutron crystallography.

Chatake, T., Shibayama, N., Park, S.Y., Kurihara, K., Tamada, T., Tanaka, I., Niimura, N., Kuroki, R., Morimoto, Y.

(2007) J Am Chem Soc 129: 14840-14841

• PubMed: 17990881 
• DOI: https://doi.org/10.1021/ja0749441
• Primary Citation of Related Structures:  
  2DXM


• PubMed Abstract: 
  

  The protonation states of buried histidine residues in human deoxyhemoglobin were unambiguously identified by using a neutron crystallographic technique. Unexpectedly, the neutron structure reveals that both the alpha- and beta-distal histidines (Hisalpha58 and Hisbeta63) adopt a positively charged, fully (doubly) protonated form, suggesting their contribution to the Bohr effect. In addition, the neutron data provide an accurate picture of the alpha1beta1 hydrogen-bonding network and allow us to observe unambiguously the nature of the intradimeric interactions at an atomic level.

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Organizational Affiliation: 

Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 64.55 kDa 
• Atom Count: 4,757 
• Modelled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C	141	Homo sapiens	Mutation(s): 0  Gene Names: HBA1, HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905 GTEx:  ENSG00000188536 ENSG00000206172

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	146	Homo sapiens	Mutation(s): 0  Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
PHAROS:  P68871 GTEx:  ENSG00000244734

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], G [auth C], H [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.260 
• R-Value Work: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.79	α = 90
b = 84.45	β = 99.33
c = 54.35	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Morimoto, Y.

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2013-08-21
  Changes: Atomic model, Other
• Version 1.3: 2018-11-28
  Changes: Data collection
• Version 1.4: 2018-12-05
  Changes: Data collection
• Version 1.5: 2024-03-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.6: 2024-04-03
  Changes: Refinement description