4G51

Crystallographic analysis of the interaction of nitric oxide with hemoglobin from Trematomus bernacchii in the T quaternary structure (fully ligated state).

PDB DOI: https://doi.org/10.2210/pdb4G51/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Trematomus bernacchii
Mutation(s): Yes

Deposited: 2012-07-17 Released: 2013-01-16
Deposition Author(s): Merlino, A., Balsamo, A., Pica, A., Mazzarella, L., Vergara, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.249
R-Value Work: 0.181
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Selective X-ray-induced NO photodissociation in haemoglobin crystals: evidence from a Raman-assisted crystallographic study.

Merlino, A., Fuchs, M.R., Pica, A., Balsamo, A., Dworkowski, F.S., Pompidor, G., Mazzarella, L., Vergara, A.

(2013) Acta Crystallogr D Biol Crystallogr 69: 137-140

PubMed: 23275172 Search on PubMed
DOI: https://doi.org/10.1107/S0907444912042229
Primary Citation of Related Structures:
4G51

PubMed Abstract:
Despite their high physiological relevance, haemoglobin crystal structures with NO bound to haem constitute less than 1% of the total ligated haemoglobins (Hbs) deposited in the Protein Data Bank. The major difficulty in obtaining NO-ligated Hbs is most likely to be related to the oxidative denitrosylation caused by the high reactivity of the nitrosylated species with O(2). Here, using Raman-assisted X-ray crystallography, it is shown that under X-ray exposure (at four different radiation doses) crystals of nitrosylated haemoglobin from Trematomus bernacchii undergo a transition, mainly in the β chains, that generates a pentacoordinate species owing to photodissociation of the Fe-NO bond. These data provide a physical explanation for the low number of nitrosylated Hb structures available in the literature.

Organizational Affiliation

Department of Chemical Sciences, University of Naples `Federico II', Italy.

Macromolecule Content

Total Structure Weight: 66.26 kDa
Atom Count: 4,729
Modelled Residue Count: 578
Deposited Residue Count: 578
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 subunit alpha	A, C	143	Trematomus bernacchii	Mutation(s): 1
UniProt
Find proteins for P80043 (Trematomus bernacchii) Explore P80043 Go to UniProtKB: P80043
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80043
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	146	Trematomus bernacchii	Mutation(s): 0
UniProt
Find proteins for P80044 (Trematomus bernacchii) Explore P80044 Go to UniProtKB: P80044
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80044
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
NO Query on NO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.249
R-Value Work: 0.181
R-Value Observed: 0.181
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.002	α = 90
b = 94.672	β = 89.16
c = 61.956	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
X-PLOR	phasing
SHELXL-97	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-16
Type: Initial release
Version 1.1: 2018-06-06
Changes: Data collection
Version 1.2: 2019-02-20
Changes: Advisory, Data collection, Derived calculations
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary