1Y8I | pdb_00001y8i

Horse methemoglobin low salt, PH 7.0 (98% relative humidity)

• PDB DOI: https://doi.org/10.2210/pdb1Y8I/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 2004-12-13 Released: 2005-07-26 
• Deposition Author(s): Sankaranarayanan, R., Biswal, B.K., Vijayan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

A new relaxed state in horse methemoglobin characterized by crystallographic studies.

Sankaranarayanan, R., Biswal, B.K., Vijayan, M.

(2005) Proteins 60: 547-551

• PubMed: 15887226 
• DOI: https://doi.org/10.1002/prot.20510
• Primary Citation Related Structures: 
  1Y8H, 1Y8I, 1Y8K


• PubMed Abstract: 
  

  A new relaxed state has been characterized in the crystals of horse methemoglobin grown at neutral pH at low ionic concentration and their low humidity variants. The crystals provide an example for improvement in X-ray diffraction quality with reduced solvent content. Only the classical R state has been so far observed in liganded horse hemoglobin. The state characterized in the present study lies in between the R state and the R2 state characterized earlier in liganded human hemoglobin. The results presented here, along with those of earlier studies, suggest that relaxed and tense hemoglobin can access ensembles of states.

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Organizational Affiliation: 
• Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

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: 64.81 kDa 
• Atom Count: 4,882 
• Modeled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin alpha chains	A, C	141	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P01958 (Equus caballus) Explore P01958  Go to UniProtKB:  P01958

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin beta chain	B, D	146	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P02062 (Equus caballus) Explore P02062  Go to UniProtKB:  P02062

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: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.798	α = 90
b = 80.907	β = 90
c = 112.159	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Sankaranarayanan, R., Biswal, B.K., Vijayan, M.

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description