[English] 日本語
Yorodumi- PDB-1ix4: Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ix4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bound to Carbon Monoxide | ||||||
Components | HEME OXYGENASE-1Heme oxygenase | ||||||
Keywords | OXIDOREDUCTASE / HEMEPROTEIN / INHIBITOR 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: 1.8 Å | ||||||
Authors | Sugishima, M. / Sakamoto, H. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Crystal Structures of Ferrous and CO-, CN(-)-, and NO-Bound Forms of Rat Heme Oxygenase-1 (HO-1) in Complex with Heme: Structural Implications for Discrimination between CO and O(2) in HO-1. Authors: Sugishima, M. / Sakamoto, H. / Noguchi, M. / Fukuyama, K. #1: Journal: J.Biol.Chem. / Year: 2003 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. / Higashimoto, Y. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ix4.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ix4.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ix4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/1ix4 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/1ix4 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30612.496 Da / Num. of mol.: 1 Fragment: soluble fragment truncated C-terminal transmembrane helix Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P06762, heme oxygenase (biliverdin-producing) |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-CMO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.65 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium formate, sodium azide, potassium formate, 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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 29, 2002 |
Radiation | Monochromator: Si(111) double-monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 28941 / Num. obs: 28311 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rsym value: 0.067 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Num. unique all: 2592 / Rsym value: 0.311 / % possible all: 91.2 |
Reflection | *PLUS Num. obs: 28853 / % possible obs: 99.7 % / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 97.4 % / Rmerge(I) obs: 0.315 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.86 Å
| |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|