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Yorodumi- PDB-3d1k: R/T intermediate quaternary structure of an antarctic fish hemogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d1k | ||||||
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Title | R/T intermediate quaternary structure of an antarctic fish hemoglobin in an alpha(CO)-beta(pentacoordinate) state | ||||||
Components | (Hemoglobin subunit ...) x 2 | ||||||
Keywords | OXYGEN BINDING / antarctic fish hemoglobin / intermediate R/T quaternary structure / oxidation pathway / Heme / Iron / Metal-binding / Oxygen transport / Transport / Acetylation | ||||||
Function / homology | Function and homology information haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / hemoglobin alpha 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Vitagliano, L. / Vergara, A. / Bonomi, G. / Merlino, A. / Mazzarella, L. | ||||||
Citation | 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. #1: Journal: Proteins / Year: 2006 Title: High resolution crystal structure of deoxy hemoglobin from Trematomus bernacchii at different pH values: the role of histidine residues in modulating the strength of the root effect. Authors: Mazzarella, L. / Vergara, A. / Vitagliano, L. / Merlino, A. / Bonomi, G. / Scala, S. / Verde, C. / di Prisco, G. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d1k.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d1k.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 3d1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d1k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3d1k_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3d1k_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 3d1k_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/3d1k ftp://data.pdbj.org/pub/pdb/validation_reports/d1/3d1k | HTTPS FTP |
-Related structure data
Related structure data | 1t1nS 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: 15677.241 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Gene HBA1 / Species: Trematomus newnesi / References: UniProt: P45718 |
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#2: Protein | Mass: 16246.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Species: Trematomus newnesi / References: UniProt: P45720 |
-Non-polymers , 4 types, 301 molecules A
#3: Chemical | #4: Chemical | ChemComp-CMO / | #5: Chemical | #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: 3.33 Å3/Da / Density % sol: 63.04 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 7.6 Details: Crysatls grew in a week by using a protein concentration of 6mg/ml and 14% w/v MPEG5000 in a 50mM Tris HCl buffer at ph 7.6, LIQUID DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Nov 4, 2000 / 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: 1.25→30 Å / Num. obs: 114368 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T1N Resolution: 1.25→30 Å / Cross valid method: troughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.25→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.29 Å / % reflection obs: 99.4 % |