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Yorodumi- PDB-4odc: Crystal structure of Trematomus bernacchii hemoglobin in a partia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4odc | ||||||
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Title | Crystal structure of Trematomus bernacchii hemoglobin in a partially cyanided state | ||||||
Components | (Hemoglobin subunit ...) x 2 | ||||||
Keywords | OXYGEN TRANSPORT/PROTEIN BINDING / alpha protein / Globin fold / oxygen transport / OXYGEN TRANSPORT-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding ...haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / 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 bernacchii (emerald rockcod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.54 Å | ||||||
Authors | Mazzarella, L. / Merlino, A. / Vitagliano, L. / Vergara, A. | ||||||
Citation | Journal: RSC ADV / Year: 2014 Title: Structural modifications induced by the switch from an endogenous bis-histidyl to an exogenous cyanomet hexa-coordination in a tetrameric haemoglobin Authors: Mazzarella, L. / Merlino, A. / Vitagliano, L. / Verde, C. / di Prisco, G. / Peisach, J. / Vergara, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4odc.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4odc.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 4odc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/4odc ftp://data.pdbj.org/pub/pdb/validation_reports/od/4odc | HTTPS FTP |
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-Related structure data
Related structure data | 2pegS 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
-Hemoglobin subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 15683.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trematomus bernacchii (emerald rockcod) / References: UniProt: P80043 |
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#2: Protein | Mass: 16153.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trematomus bernacchii (emerald rockcod) / References: UniProt: P80044 |
-Non-polymers , 4 types, 410 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.33 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 7.6 Details: Crystallization of partially cyanided HbTb (CN-HbTb) was carried out at pH 7.6 and room temperature via liquid-diffusion technique, using a capillary. Precipitant solution: 10% (w/v) PEG MME ...Details: Crystallization of partially cyanided HbTb (CN-HbTb) was carried out at pH 7.6 and room temperature via liquid-diffusion technique, using a capillary. Precipitant solution: 10% (w/v) PEG MME 5000, 50 mM TRIS-HCl pH 7.6, LIQUID DIFFUSION, temperature 293K |
-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: May 27, 2003 |
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: 1.54→30 Å / Num. all: 61743 / Num. obs: 61743 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.042 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 2peg Resolution: 1.54→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.54→30 Å
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