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- PDB-1j2c: Crystal structure of rat heme oxygenase-1 in complex with biliver... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j2c | ||||||
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Title | Crystal structure of rat heme oxygenase-1 in complex with biliverdin IXalpha-iron cluster | ||||||
![]() | Heme Oxygenase-1 | ||||||
![]() | OXIDOREDUCTASE / ENZYME-PRODUCT complex / BENT HELIX | ||||||
Function / homology | ![]() Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonic acid / heme metabolic process / phospholipase D activity ...Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonic acid / heme metabolic process / phospholipase D activity / heme oxygenase (biliverdin-producing) / cellular response to cisplatin / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / negative regulation of muscle cell apoptotic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of mast cell cytokine production / heme catabolic process / cellular response to arsenic-containing substance / cellular response to nutrient / negative regulation of epithelial cell apoptotic process / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / epithelial cell apoptotic process / positive regulation of cell migration involved in sprouting angiogenesis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / caveola / liver regeneration / macroautophagy / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / response to nicotine / response to hydrogen peroxide / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to heat / cellular response to hypoxia / angiogenesis / intracellular iron ion homeostasis / response to oxidative stress / negative regulation of neuron apoptotic process / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / structural molecule activity / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugishima, M. / Sakamoto, H. / Noguchi, M. / Fukuyama, K. | ||||||
![]() | ![]() Title: Crystal Structure of Rat Heme Oxygenase-1 in Complex with Biliverdin-Iron Chelate: CONFORMATIONAL CHANGE OF THE DISTAL HELIX DURING THE HEME CLEAVAGE REACTION. Authors: Sugishima, M. / Sakamoto, H. / Higashimoto, Y. / Noguchi, M. / Fukuyama, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.4 KB | Display | ![]() |
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PDB format | ![]() | 42.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 782.4 KB | Display | ![]() |
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Full document | ![]() | 785 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ix3S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assmbly is a monomer. |
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Components
#1: Protein | Mass: 30612.496 Da / Num. of mol.: 1 / Fragment: C-terminal truncated protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P06762, heme oxygenase (biliverdin-producing) |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-BLA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.36 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium formate, potassium phosphate, potassium cyanide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Sugishima, M., (2002) J.Biol.Chem., 277, 45086. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 23, 2002 |
Radiation | Monochromator: Si (111) double monochrmator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→60.9 Å / Num. all: 12241 / Num. obs: 12207 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.09 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1726 / Rsym value: 0.343 / % possible all: 99.5 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 88285 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.343 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IX3 Resolution: 2.4→60.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→60.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å
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Refinement | *PLUS Lowest resolution: 50 Å | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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