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Yorodumi- PDB-1ivj: Crystal Structure of Rat Hemeoxygenase-1 in Complex with Heme and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ivj | ||||||
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Title | Crystal Structure of Rat Hemeoxygenase-1 in Complex with Heme and Azide. | ||||||
Components | Hemeoxygenase-1 | ||||||
Keywords | OXIDOREDUCTASE / ALPHA HELIX / DI-OXYGEN ANALOG COMPLEX | ||||||
Function / homology | Function and homology information 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 / heme metabolic process / response to arachidonic acid / 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 / heme metabolic process / response to arachidonic acid / 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 / erythrocyte homeostasis / positive regulation of epithelial cell apoptotic process / epithelial cell apoptotic process / negative regulation of macroautophagy / small GTPase-mediated signal transduction / positive regulation of cell migration involved in sprouting angiogenesis / 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 / response to nicotine / caveola / liver regeneration / negative regulation of smooth muscle cell proliferation / macroautophagy / positive regulation of smooth muscle cell proliferation / 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 / response to oxidative stress / intracellular iron ion homeostasis / 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 / perinuclear region of cytoplasm / structural molecule activity / enzyme binding / endoplasmic reticulum / protein homodimerization activity / identical protein binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sugishima, M. / Sakamoto, H. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal Structure of Rat Heme Oxygenase-1 in Complex with Heme Bound to Azide. IMPLICATION FOR REGIOSPECIFIC HYDROXYLATION OF HEME AT THE alpha -MESO CARBON Authors: Sugishima, M. / Sakamoto, H. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ivj.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ivj.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ivj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1ivj ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1ivj | HTTPS FTP |
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-Related structure data
Related structure data | 1dveS 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: 30612.496 Da / Num. of mol.: 1 / Fragment: TRANS-MEMBRANE REGION Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) References: UniProt: P06762, heme oxygenase (biliverdin-producing) | ||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #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: 2.68 Å3/Da / Density % sol: 53.79 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium formate, pottasium phosphate, sodium azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2002 |
Radiation | Monochromator: Si(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 23849 / Num. obs: 23376 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.25 % / Rsym value: 0.054 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique all: 1157 / Rsym value: 0.325 / % possible all: 96.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 23376 / Num. measured all: 169506 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.325 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DVE Resolution: 1.9→20 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: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.26 |