+Open data
-Basic information
Entry | Database: PDB / ID: 1t1n | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN | ||||||
Components | (PROTEIN (HEMOGLOBIN)) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / HEMOGLOBIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Mazzarella, L. / Vitagliano, L. / Savino, C. / Zagari, A. | ||||||
Citation | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1t1n.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1t1n.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 1t1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/1t1n ftp://data.pdbj.org/pub/pdb/validation_reports/t1/1t1n | HTTPS FTP |
---|
-Related structure data
Related structure data | 1pbxS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15703.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HEM GROUP IS COMPLEXED WITH CARBON MONOXIDE / Source: (natural) Trematomus newnesi (dusky notothen) / Cell: RED BLOOD CELLS / Tissue: BLOOD / References: UniProt: P45718 | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 16246.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HEM GROUP IS COMPLEXED WITH CARBON MONOXIDE / Source: (natural) Trematomus newnesi (dusky notothen) / Cell: RED BLOOD CELLS / Tissue: BLOOD / References: UniProt: P45720 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: microdialysis | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 15, 1993 / Details: COLLIMATOR |
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: 2.1→50 Å / Num. obs: 25207 / % possible obs: 99.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.1→2.2 Å / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 68936 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PBX Resolution: 2.2→16 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|