3BOM

Crystal structure of trout hemoglobin at 1.35 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb3BOM/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Oncorhynchus mykiss
• Mutation(s): No 


• Deposited: 2007-12-17 Released: 2008-01-08 
• Deposition Author(s): Aranda IV, R., Bingman, C.A., Bitto, E., Wesenberg, G.E., Richards, M., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.212 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Trout Hemoglobin Crystal Structure at 1.35 Angstroms Resolution.

Aranda IV, R., Bingman, C.A., Bitto, E., Wesenberg, G.E., Richards, M., Phillips Jr., G.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: 66.49 kDa 
• Atom Count: 5,636 
• Modelled Residue Count: 580 
• Deposited Residue Count: 580 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha-4	A, C	143	Oncorhynchus mykiss	Mutation(s): 0
UniProt
Find proteins for P14527 (Oncorhynchus mykiss) Explore P14527  Go to UniProtKB:  P14527

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta-4	B, D	147	Oncorhynchus mykiss	Mutation(s): 0
UniProt
Find proteins for P02141 (Oncorhynchus mykiss) Explore P02141  Go to UniProtKB:  P02141

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], H [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
EDO	G [auth B], I [auth C], J [auth C], L [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.212 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.455	α = 90
b = 63.162	β = 93.1
c = 78.702	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-08 
Deposition Author(s): Aranda IV, R., Bingman, C.A., Bitto, E., Wesenberg, G.E., Richards, M., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2008-01-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-01-23
  Changes: Database references, Structure summary
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary