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Yorodumi- PDB-1j2c: Crystal structure of rat heme oxygenase-1 in complex with biliver... -
+Open data
-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 | ||||||
Components | Heme Oxygenase-1Heme oxygenase | ||||||
Keywords | OXIDOREDUCTASE / ENZYME-PRODUCT complex / BENT HELIX | ||||||
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: 2.4 Å | ||||||
Authors | Sugishima, M. / Sakamoto, H. / Noguchi, M. / Fukuyama, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j2c.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j2c.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 1j2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/1j2c ftp://data.pdbj.org/pub/pdb/validation_reports/j2/1j2c | HTTPS FTP |
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-Related structure data
Related structure data | 1ix3S 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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Details | The biological assmbly is a monomer. |
-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.) Rattus norvegicus (Norway rat) / Plasmid: pBAce / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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