3PI3

Crystallographic Structure of HbII-oxy from Lucina pectinata at pH 5.0

• PDB DOI: https://doi.org/10.2210/pdb3PI3/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Phacoides pectinatus
• Mutation(s): Yes 


• Deposited: 2010-11-05 Released: 2011-11-09 
• Deposition Author(s): Gavira, J.A., Nieves-Marrero, C.A., Ruiz-Martinez, C.R., Estremera-Andujar, R.A., Lopez-Garriga, J., Garcia-Ruiz, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

pH-dependence crystallographic studies of the oxygen carrier hemoglobin II from Lucina pectinata

Nieves-Marrero, C.A., Ruiz-Martinez, C.R., Estremera-Andujar, R.A., Lopez-Garriga, J., Garcia-Ruiz, J.M., Gavira, J.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.38 kDa 
• Atom Count: 2,810 
• Modelled Residue Count: 304 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin II	A, B	152	Phacoides pectinatus	Mutation(s): 1
UniProt
Find proteins for P41261 (Phacoides pectinatus) Explore P41261  Go to UniProtKB:  P41261

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
OXY	D [auth A], F [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.973	α = 90
b = 73.973	β = 90
c = 153.194	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Gavira, J.A., Nieves-Marrero, C.A., Ruiz-Martinez, C.R., Estremera-Andujar, R.A., Lopez-Garriga, J., Garcia-Ruiz, J.M.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary