6HIT

The crystal structure of haemoglobin from Atlantic cod

PDB DOI: https://doi.org/10.2210/pdb6HIT/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Gadus morhua
Mutation(s): Yes

Deposited: 2018-08-30 Released: 2019-08-21
Deposition Author(s): Helland, R., Bjorkeng, E.K., Rothweiler, U., Sydnes, M.O., Pampanin, D.M.
Funding Organization(s): Research Council of Norway

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.301
R-Value Work: 0.232
R-Value Observed: 0.236

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of haemoglobin from Atlantic cod.

Helland, R., Bjorkeng, E.K., Rothweiler, U., Sydnes, M.O., Pampanin, D.M.

(2019) Acta Crystallogr F Struct Biol Commun 75: 537-542

PubMed: 31397324 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X1900904X
Primary Citation of Related Structures:
6HIT

PubMed Abstract:
The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 Å resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly.

Organizational Affiliation

NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway.

Macromolecule Content

Total Structure Weight: 133.16 kDa
Atom Count: 8,834
Modelled Residue Count: 1,151
Deposited Residue Count: 1,152
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin alpha 2 chain	A, C, E, G	143	Gadus morhua	Mutation(s): 1
UniProt
Find proteins for O42425 (Gadus morhua) Explore O42425 Go to UniProtKB: O42425
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O42425
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin beta 4 chain	B, D, F, H	145	Gadus morhua	Mutation(s): 0
UniProt
Find proteins for B3F9D7 (Gadus morhua) Explore B3F9D7 Go to UniProtKB: B3F9D7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3F9D7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain N [auth F] SDF format, chain I [auth A] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain O [auth G] SDF format, chain P [auth H] MOL2 format, chain J [auth B] MOL2 format, chain N [auth F] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain O [auth G] MOL2 format, chain P [auth H]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.301
R-Value Work: 0.232
R-Value Observed: 0.236
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.691	α = 90
b = 103.257	β = 90
c = 199.352	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Council of Norway	Norway	229153
Research Council of Norway	Norway	247732

Revision History (Full details and data files)

Version 1.0: 2019-08-21
Type: Initial release
Version 1.1: 2024-05-01
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description