5EUI | pdb_00005eui

Structure of predicted ancestral pika hemoglobin

• PDB DOI: https://doi.org/10.2210/pdb5EUI/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Ochotona princeps
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-18 Released: 2016-11-30 
• Deposition Author(s): Inoguchi, N., Chandrasekhar, N., Storz, J.F., Moriyama, H.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

structure of predicted pika ancestral hemoglobin at 1.45 Angstroms resolution.

Inoguchi, N., Natarajan, C., Storz, J.F., Moriyama, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 32.32 kDa 
• Atom Count: 2,703 
• Modeled Residue Count: 280 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HBA protein	A	141	Ochotona princeps	Mutation(s): 0  Gene Names: HBA
UniProt
Find proteins for U5KQB1 (Ochotona princeps) Explore U5KQB1  Go to UniProtKB:  U5KQB1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HBB protein	B	146	Ochotona princeps	Mutation(s): 0  Gene Names: HBB
UniProt
Find proteins for U5KNG4 (Ochotona princeps) Explore U5KNG4  Go to UniProtKB:  U5KNG4

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: 1.45 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.35	α = 90
b = 91.412	β = 90
c = 103.537	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-30 
Deposition Author(s): Inoguchi, N., Chandrasekhar, N., Storz, J.F., Moriyama, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL087216-07
National Science Foundation (NSF, United States)	United States	MCB-151763 6

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description