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- PDB-4esa: X-ray structure of carbonmonoxy hemoglobin of Eleginops maclovinus -

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Basic information

Entry
Database: PDB / ID: 4esa
TitleX-ray structure of carbonmonoxy hemoglobin of Eleginops maclovinus
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN TRANSPORT / haemoglobin / ligand-binding properties / Root effect / quaternary structure / structure/function relationship / oxygen transporter / O2 / blood
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha 1 / Hemoglobin subunit beta-1
Similarity search - Component
Biological speciesEleginops maclovinus (Patagonian blennie)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMerlino, A. / Vitagliano, L. / Mazzarella, L. / Vergara, A.
Citation
Journal: Mol Biosyst / Year: 2012
Title: ATP regulation of the ligand-binding properties in temperate and cold-adapted haemoglobins. X-ray structure and ligand-binding kinetics in the sub-Antarctic fish Eleginops maclovinus.
Authors: Coppola, D. / Abbruzzetti, S. / Nicoletti, F. / Merlino, A. / Gambacurta, A. / Giordano, D. / Howes, B.D. / De Sanctis, G. / Vitagliano, L. / Bruno, S. / di Prisco, G. / Mazzarella, L. / ...Authors: Coppola, D. / Abbruzzetti, S. / Nicoletti, F. / Merlino, A. / Gambacurta, A. / Giordano, D. / Howes, B.D. / De Sanctis, G. / Vitagliano, L. / Bruno, S. / di Prisco, G. / Mazzarella, L. / Smulevich, G. / Coletta, M. / Viappiani, C. / Vergara, A. / Verde, C.
#1: Journal: Biopolymers / Year: 2009
Title: Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins.
Authors: Merlino, A. / Vitagliano, L. / Howes, B.D. / Verde, C. / di Prisco, G. / Smulevich, G. / Sica, F. / Vergara, A.
#2: Journal: J.Am.Chem.Soc. / Year: 2008
Title: Spectroscopic and crystallographic characterization of a tetrameric hemoglobin oxidation reveals structural features of the functional intermediate relaxed/tense state.
Authors: Vitagliano, L. / Vergara, A. / Bonomi, G. / Merlino, A. / Verde, C. / di Prisco, G. / Howes, B.D. / Smulevich, G. / Mazzarella, L.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin alpha chain
B: Hemoglobin beta chain
C: Hemoglobin alpha chain
D: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,34913
Polymers63,6794
Non-polymers2,6709
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12800 Å2
ΔGint-112 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.175, 88.075, 123.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Hemoglobin alpha chain


Mass: 15686.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Eleginops maclovinus (Patagonian blennie) / References: UniProt: K7N5M5*PLUS
#2: Protein Hemoglobin beta chain


Mass: 16153.450 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Eleginops maclovinus (Patagonian blennie) / References: UniProt: K7N5M6*PLUS

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Non-polymers , 4 types, 417 molecules

#3: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 8
Details: 10 ml protein solution at 20 mg/ml 1 in 100 mM Tris HCl buffer and 2 mM sodium dithionite was dialyzed against a 25 ml reservoir containing 2 M ammonium sulfate, 100 mM Tris HCl, 2 mM sodium ...Details: 10 ml protein solution at 20 mg/ml 1 in 100 mM Tris HCl buffer and 2 mM sodium dithionite was dialyzed against a 25 ml reservoir containing 2 M ammonium sulfate, 100 mM Tris HCl, 2 mM sodium dithionite, pH 8.0, MICRODIALYSIS, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 4, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 109738 / Num. obs: 109671 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 37.5
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.3 / % possible all: 90.8

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
SHELXLrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3gkv

3gkv


Resolution: 1.45→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.253 7491 RANDOM
Rwork0.212 --
all0.214 109671 -
obs0.212 109671 -
Solvent computationSolvent model: THE AUTHORS USED ALL REFLECTIONS FOR THE LAST REFINEMENT. THE RFREE SET HAS BEEN REINTRODUCED FOR DEPOSITION PURPOSES.
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 186 408 5046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d2.008

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