[English] 日本語
Yorodumi- PDB-3gqg: Crystal structure at acidic pH of the ferric form of the Root eff... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gqg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure at acidic pH of the ferric form of the Root effect hemoglobin from Trematomus bernacchii. | ||||||
Components |
| ||||||
Keywords | OXYGEN TRANSPORT / pentacoordinate high-spin Fe(III) form / antacrtic fish hemoglobin / Acetylation / Heme / Iron / Metal-binding / Transport | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Vergara, A. / Franzese, M. / Merlino, A. / Bonomi, G. / Mazzarella, L. | ||||||
Citation | Journal: Biophys.J. / Year: 2009 Title: Correlation between hemichrome stability and the root effect in tetrameric hemoglobins. Authors: Vergara, A. / Franzese, M. / Merlino, A. / Bonomi, G. / Verde, C. / Giordano, D. / di Prisco, G. / Lee, H.C. / Peisach, J. / Mazzarella, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gqg.cif.gz | 137 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gqg.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gqg_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3gqg_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3gqg_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3gqg_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/3gqg ftp://data.pdbj.org/pub/pdb/validation_reports/gq/3gqg | HTTPS FTP |
-Related structure data
Related structure data | 2h8fS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | tetramer |
-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-HEM / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.62 % |
---|---|
Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6 Details: Crystallization of oxidized Hb from trematomus bernacchii was carried out in capillary at pH6 and room temperature by liquid diffusion technique (final crystallization conditions were 1.5 ...Details: Crystallization of oxidized Hb from trematomus bernacchii was carried out in capillary at pH6 and room temperature by liquid diffusion technique (final crystallization conditions were 1.5 mg/ml protein and 8% w/v MPEG 5K)., pH 6.0, LIQUID DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 14, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→13.9 Å / Num. all: 69281 / Num. obs: 69281 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.73→1.76 Å / Rmerge(I) obs: 0.175 / % possible all: 88.1 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 2H8F Resolution: 1.73→13.9 Å Isotropic thermal model: Isotropic. Anisotropic thermal model has been used for iron atoms. Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Please note that the collected diffraction data show pseudo-merohedral twinning. The twin fractions, determined by the algorithm implemented in the progream SHELX is almost 0.50.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→13.9 Å
|