3DHT | pdb_00003dht

The Crystal Structure Determination of Rat (rattus norvegicus) Hemoglobin

• PDB DOI: https://doi.org/10.2210/pdb3DHT/pdb

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


• Deposited: 2008-06-18 Released: 2009-06-30 
• Deposition Author(s): Neelagandan, K., Sathya Moorthy, P., Balasubramanian, M., Sundaresan, S., Ponnuswamy, M.N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 
  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure Determination of Rat (rattus norvegicus) Hemoglobin

Neelagandan, K., Sathya Moorthy, P., Balasubramanian, M., Sundaresan, S., 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.

Macromolecule Content 

• Total Structure Weight: 32.33 kDa 
• Atom Count: 2,255 
• Modeled Residue Count: 284 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-1/2	A	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	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	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.71	α = 90
b = 53.71	β = 90
c = 350.32	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
AUTOMAR	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Neelagandan, K., Sathya Moorthy, P., Balasubramanian, M., Sundaresan, S., Ponnuswamy, M.N.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-10
  Changes: Derived calculations
• Version 1.3: 2016-12-21
  Changes: Other
• Version 1.4: 2017-10-25
  Changes: Refinement description
• Version 1.5: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description