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Yorodumi- PDB-2aa1: Crystal structure of the cathodic hemoglobin isolated from the An... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aa1 | ||||||
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Title | Crystal structure of the cathodic hemoglobin isolated from the Antarctic fish Trematomus Newnesi | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / hemoglobin / Root effect / cooperativity / Antarctic fish / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / 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 | ||||||
Biological species | Trematomus newnesi (dusky notothen) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Mazzarella, L. / Bonomi, G. / Lubrano, M.C. / Merlino, A. / Riccio, A. / Vergara, A. / Vitagliano, L. / Verde, C. / Di Prisco, G. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Minimal structural requirements for root effect: crystal structure of the cathodic hemoglobin isolated from the antarctic fish Trematomus newnesi Authors: Mazzarella, L. / Bonomi, G. / Lubrano, M.C. / Merlino, A. / Riccio, A. / Vergara, A. / Vitagliano, L. / Verde, C. / di Prisco, G. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of Trematomus newnesi haemoglobin re-opens the root effect question Authors: Mazzarella, L. / D'Avino, R. / di Prisco, G. / Savino, C. / Vitagliano, L. / Moody, P.C.E. / Zagari, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aa1.cif.gz | 135.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aa1.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 2aa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/2aa1 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/2aa1 | HTTPS FTP |
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-Related structure data
Related structure data | 1hbhS 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
#1: Protein | Mass: 15703.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trematomus newnesi (dusky notothen) / References: UniProt: P45718 #2: Protein | Mass: 16277.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trematomus newnesi (dusky notothen) / References: UniProt: P45721 #3: Chemical | ChemComp-HEM / #4: 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: 2.94 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 9-12%(w/v) PEG 6000, phosphate buffer, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection shell | Resolution: 1.8→1.88 Å / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HBH Resolution: 1.8→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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