3HF4 | pdb_00003hf4

Crystal structure of rat methemoglobin in R2 state

• PDB DOI: https://doi.org/10.2210/pdb3HF4/pdb

• Classification: OXYGEN STORAGE, OXYGEN TRANSPORT
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2009-05-11 Released: 2010-05-19 
• Deposition Author(s): Neelagandan, K., Sathya Moorthy, P., Balasubramanian, M., Ponnuswamy, M.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Quaternary structural variability in rat hemoglobin

Neelagandan, K., Sathya Moorthy, P., Balasubramanian, M., Ponnuswamy, M.N.

To be published.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.66 kDa 
• Atom Count: 4,554 
• Modeled Residue Count: 573 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-1/2	A, C [auth E]	141	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P01946 (Rattus norvegicus) Explore P01946  Go to UniProtKB:  P01946

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta-1	B, D [auth F]	146	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P02091 (Rattus norvegicus) Explore P02091  Go to UniProtKB:  P02091

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.14	α = 90
b = 54.015	β = 93.8
c = 115.008	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
AUTOMAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Neelagandan, K., Sathya Moorthy, P., Balasubramanian, M., Ponnuswamy, M.N.

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2018-06-20
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2020-01-15
  Changes: Advisory, Derived calculations
• Version 1.6: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description