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Yorodumi- PDB-3gdj: Crystal structure determination of camel(Camelus dromedarius)hemo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gdj | ||||||
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Title | Crystal structure determination of camel(Camelus dromedarius)hemoglobin at 2 angstrom resolution | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / Methemoglobin / HIGH OXYGEN AFFINITY / CHROMATOGRAPHY / MONOCLINIC. / Heme / Iron / Metal-binding / Transport | ||||||
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 | Camelus dromedarius (Arabian camel) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Balasubramanian, M. / Sathya Moorthy, P. / Neelagandan, K. / Ponnuswamy, M.N. | ||||||
Citation | Journal: To be Published Title: Crystal structure determination of camel(Camelus dromedarius)hemoglobin at 2 angstrom resolution Authors: Balasubramanian, M. / Sathya Moorthy, P. / Neelagandan, 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 | 3gdj.cif.gz | 131.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gdj.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/3gdj ftp://data.pdbj.org/pub/pdb/validation_reports/gd/3gdj | HTTPS FTP |
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-Related structure data
Related structure data | 2pghS 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
#1: Protein | Mass: 15199.341 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Camelus dromedarius (Arabian camel) / Tissue: BLOOD-ERYTHROCYTES(RBC) / References: UniProt: P63106 #2: Protein | Mass: 16140.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Camelus dromedarius (Arabian camel) / Tissue: BLOOD-ERYTHROCYTES(RBC) / References: UniProt: P68231 #3: Chemical | ChemComp-HEM / #4: 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: 2.25 Å3/Da / Density % sol: 45.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.003ml of protein solution with 0.002ml of 45% PEG 3350 in 50mM of phosphate buffer at pH 6.8 with 1 M NaCl equilibrated against 1 ml of reservoir containing the same solution, VAPOR ...Details: 0.003ml of protein solution with 0.002ml of 45% PEG 3350 in 50mM of phosphate buffer at pH 6.8 with 1 M NaCl equilibrated against 1 ml of reservoir containing the same solution, VAPOR DIFFUSION, HANGING DROP, temperature 293KK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5417 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 19, 2009 / Details: mirrors |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 87740 / Num. obs: 35552 / % possible obs: 94.2 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 2.43 % / Rmerge(I) obs: 0.0774 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.3202 / Mean I/σ(I) obs: 1 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PGH Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.61 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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