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Yorodumi- PDB-1s0h: Structure determination of haemoglobin from Donkey(equus asinus) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s0h | ||||||
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Title | Structure determination of haemoglobin from Donkey(equus asinus) at 3.0 Angstrom resolution | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / alpha helix / dimer / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Equus asinus (ass) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Balasundaresan, D. / Ponnuswamy, M.N. / Saraboji, K. | ||||||
Citation | Journal: Biochimie / Year: 2006 Title: Crystal structure of haemoglobin from donkey (Equus asinus) at 3A resolution Authors: Balasundaresan, D. / Saraboji, K. / Ponnuswamy, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s0h.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s0h.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 1s0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/1s0h ftp://data.pdbj.org/pub/pdb/validation_reports/s0/1s0h | HTTPS FTP |
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-Related structure data
Related structure data | 2mhbS 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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Details | TO GENERATE COORDINATES FOR THE ALPHA-2 AND BETA-2 CHAINS FROM THE ALPHA-1 AND BETA-1 COORDINATES GIVEN HERE, APPLY THE OPERATION: -x,y,-z |
-Components
#1: Protein | Mass: 15098.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus asinus (ass) / Cell: Erythrocytes / References: UniProt: P01959 |
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#2: Protein | Mass: 16032.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus asinus (ass) / Cell: Erythrocytes / References: UniProt: D1MPT0*PLUS |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 2.8M Na/K phosphate buffer, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 8, 2003 / Details: Monochromator |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.002→30 Å / Num. all: 5406 / Num. obs: 5387 / % possible obs: 79.01 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 3.002→3.079 Å / Rmerge(I) obs: 0.43 / Num. unique all: 584 / % possible all: 34.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Horse Methaemoglobin(PDB ID:2MHB) Resolution: 3→21.18 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.828 / SU B: 32.603 / SU ML: 0.545 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.628 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.322 Å2
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Refinement step | Cycle: LAST / Resolution: 3→21.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.002→3.079 Å / Total num. of bins used: 20
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