+Open data
-Basic information
Entry | Database: PDB / ID: 1dke | ||||||
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Title | NI BETA HEME HUMAN HEMOGLOBIN | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / Late endosomal microautophagy / oxygen carrier activity / carbon dioxide transport / Heme signaling / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / regulation of blood pressure / platelet aggregation / oxygen binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Bruno, S. / Bettatti, S. / Mozzarelli, A. / Bolognesi, M. / Deriu, D. / Rosano, C. / Tsuneshige, A. / Yonetani, T. / Henry, E.R. | ||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Oxygen binding by alpha(Fe2+)2beta(Ni2+)2 hemoglobin crystals. Authors: Bruno, S. / Bettati, S. / Manfredini, M. / Mozzarelli, A. / Bolognesi, M. / Deriu, D. / Rosano, C. / Tsuneshige, A. / Yonetani, T. / Henry, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dke.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dke.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dke ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dke | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BETA HEME CONTAINS NI+2 ION / Source: (natural) Homo sapiens (human) / Keywords: BETA HEME CONTAINS NI+2 ION / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-SO4 / | #5: 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: 2.28 Å3/Da / Density % sol: 46.16 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 24 MG/ML PROTEIN 21% PEG 1000 10MM POTASSIUM PHOSPHATE, 1MM IHP, 30MM SODIUM DITHIONITE, pH 7, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→22.5 Å / Num. all: 32068 / Num. obs: 32068 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.159 / % possible all: 95.7 |
Reflection | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Resolution: 2.1→12 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.1→12 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_plane_restr / Dev ideal: 0.046 |