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Yorodumi- PDB-3dht: The Crystal Structure Determination of Rat (rattus norvegicus) He... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dht | ||||||
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Title | The Crystal Structure Determination of Rat (rattus norvegicus) Hemoglobin | ||||||
Components |
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Keywords | OXYGEN STORAGE / OXYGEN TRANSPORT / Hemoglobin / heme / Iron / Metal-binding / Transport / Phosphoprotein | ||||||
Function / homology | Function and homology information Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Heme signaling / hemoglobin beta binding / regulation of eIF2 alpha phosphorylation by heme / response to stilbenoid / cellular oxidant detoxification / Cytoprotection by HMOX1 / nitric oxide transport ...Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Scavenging of heme from plasma / Heme signaling / hemoglobin beta binding / regulation of eIF2 alpha phosphorylation by heme / response to stilbenoid / cellular oxidant detoxification / Cytoprotection by HMOX1 / nitric oxide transport / Neutrophil degranulation / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / hemopoiesis / erythrocyte development / negative regulation of blood pressure / glutathione metabolic process / hydrogen peroxide catabolic process / oxygen carrier activity / response to bacterium / carbon dioxide transport / response to hydrogen peroxide / oxygen binding / amyloid-beta binding / in utero embryonic development / iron ion binding / heme binding / protein-containing complex binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Neelagandan, K. / Sathya Moorthy, P. / Balasubramanian, M. / Sundaresan, S. / Ponnuswamy, M.N. | ||||||
Citation | Journal: To be Published Title: The Crystal Structure Determination of Rat (rattus norvegicus) Hemoglobin Authors: Neelagandan, K. / Sathya Moorthy, P. / Balasubramanian, M. / Sundaresan, S. / Ponnuswamy, M.N. #1: Journal: Protein Pept.Lett. / Year: 2003 Title: Crystal structure of hemoglobin from the maned wolf (Chrysocyon brachyurus) using synchrotron radiation Authors: Fadel, V. / Canduri, F. / Olivieri, J.R. / Smarra, A.L.S. / Colombo, M.F. / Bonilla-Rodriguez, G.O. / de Azevedo, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dht.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dht.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 3dht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dht_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3dht_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3dht_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3dht_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/3dht ftp://data.pdbj.org/pub/pdb/validation_reports/dh/3dht | HTTPS FTP |
-Related structure data
Related structure data | 1fhjS 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: 15222.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Cell: red blood cell / References: UniProt: P01946 | ||
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#2: Protein | Mass: 15873.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Cell: red blood cell / References: UniProt: P02091 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 40% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5478 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: NIL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5478 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→30 Å / Num. all: 6233 / Num. obs: 6233 / Redundancy: 14.3 % / Rsym value: 0.2132 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.97→3.08 Å / Redundancy: 11.5 % / Rsym value: 0.3962 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FHJ Resolution: 2.98→23.26 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.846 / SU B: 16.984 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.556 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.98→23.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.975→3.051 Å / Total num. of bins used: 20
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