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Yorodumi- PDB-4iro: Crystal structure of T-state carbonmonoxy hemoglobin from Tremato... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iro | ||||||
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Title | Crystal structure of T-state carbonmonoxy hemoglobin from Trematomus bernacchii at pH 8.4 | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / Globin fold | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Merlino, A. / Balsamo, A. / Mazzarella, L. / Vergara, A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Role of tertiary structures on the Root effect in fish hemoglobins. Authors: Ronda, L. / Merlino, A. / Bettati, S. / Verde, C. / Balsamo, A. / Mazzarella, L. / Mozzarelli, A. / Vergara, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iro.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iro.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 4iro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/4iro ftp://data.pdbj.org/pub/pdb/validation_reports/ir/4iro | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 15683.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trematomus bernacchii (emerald rockcod) / References: UniProt: P80043 #2: Protein | Mass: 16153.368 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trematomus bernacchii (emerald rockcod) / References: UniProt: P80044 #3: Chemical | ChemComp-CMO / | #4: Chemical | ChemComp-HEM / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: deoxy-HbTb crystals have been grown using 8-9.5 mg/ml protein mixed with equal amount of 7-12 % w/v PEG 6000, PBS 100 mM, KCl 0.3 M, pH 8.4. Deoxy HbTb crystals were then soaked for several ...Details: deoxy-HbTb crystals have been grown using 8-9.5 mg/ml protein mixed with equal amount of 7-12 % w/v PEG 6000, PBS 100 mM, KCl 0.3 M, pH 8.4. Deoxy HbTb crystals were then soaked for several hours in a deoxygenated, CO saturated, stabilizing solution containing 30% w/v PEG 6000, 100 mM Trsi-HCl pH 8.4, 200 mM KCl, 5 mM dithionite reducing agent and flushed with gaseous CO before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 27, 2010 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→72.165 Å / Num. all: 34835 / Num. obs: 34835 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→72.165 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: DIFFRACTION DATA WERE COLLEXCTED ON TWO SINGLE CRYSTALS. THE TWO DATA SET WERE INDEXED, PROCESSED AND SCALED WITH HKL2000. THE AGREEMENT BETWEEN THE TWO DATA SETS WAS OF THE ORDER OF THE ...Details: DIFFRACTION DATA WERE COLLEXCTED ON TWO SINGLE CRYSTALS. THE TWO DATA SET WERE INDEXED, PROCESSED AND SCALED WITH HKL2000. THE AGREEMENT BETWEEN THE TWO DATA SETS WAS OF THE ORDER OF THE EXPECTED ERRORS (RMERGE 0.069). FOR EACH DATA SET, THE STRUCTURE WAS REFINED WITH SHELX PROGRAM. SINCE ALL THE BASIC FEATURES, SUCH AS THE COORDINATION AT THE HEME IRONS, SUBSTANTIALLY AGREE IN THE TWO STRUCTURES THE TWO DATA SETS WERE MERGED FOR SUCCESSIVE REFINEMENT STEPS. ALL REFLECTION WERE USED FOR REFINEMENT
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Refinement step | Cycle: LAST / Resolution: 2.2→72.165 Å
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