4YU4 | pdb_00004yu4

Crystal structure of Mongoose (Helogale parvula) hemoglobin at pH 7.0

• PDB DOI: https://doi.org/10.2210/pdb4YU4/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Helogale parvula
• Mutation(s): No 


• Deposited: 2015-03-18 Released: 2015-09-23 
• Deposition Author(s): Abubakkar, M.M., Maheshwaran, V., Ponnuswamy, M.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.227 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.163 (Depositor) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Mongoose (Helogale parvula) hemoglobin at pH 7.0

Abubakkar, M.M., Maheshwaran, V., 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: 65.17 kDa 
• Atom Count: 4,658 
• Modeled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemoglobin	A, C	141	Helogale parvula	Mutation(s): 0
UniProt
Find proteins for A0A0R4I977 (Helogale parvula) Explore A0A0R4I977  Go to UniProtKB:  A0A0R4I977

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hemoglobin	B, D	146	Helogale parvula	Mutation(s): 0
UniProt
Find proteins for A0A0R4I978 (Helogale parvula) Explore A0A0R4I978  Go to UniProtKB:  A0A0R4I978

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.227 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.163 (Depositor) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.92	α = 90
b = 88.21	β = 90
c = 129.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Abubakkar, M.M., Maheshwaran, V., Ponnuswamy, M.N.

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description