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Yorodumi- PDB-4esa: X-ray structure of carbonmonoxy hemoglobin of Eleginops maclovinus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4esa | ||||||
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Title | X-ray structure of carbonmonoxy hemoglobin of Eleginops maclovinus | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / haemoglobin / ligand-binding properties / Root effect / quaternary structure / structure/function relationship / oxygen transporter / O2 / blood | ||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Eleginops maclovinus (Patagonian blennie) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Merlino, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4esa.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4esa.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 4esa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4esa_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4esa_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4esa_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4esa_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/4esa ftp://data.pdbj.org/pub/pdb/validation_reports/es/4esa | HTTPS FTP |
-Related structure data
Related structure data | 3gkvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | 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 | 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 / #4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.36 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 4, 2009 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.45→1.5 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.3 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3gkv Resolution: 1.45→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: THE AUTHORS USED ALL REFLECTIONS FOR THE LAST REFINEMENT. THE RFREE SET HAS BEEN REINTRODUCED FOR DEPOSITION PURPOSES. | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→50 Å
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Refine LS restraints |
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