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Yorodumi- PDB-1dvg: CRYSTAL STRUCTURE OF RAT HEME OXYGENASE-1 IN COMPLEX WITH HEME; S... -
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-Basic information
Entry | Database: PDB / ID: 1dvg | ||||||
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Title | CRYSTAL STRUCTURE OF RAT HEME OXYGENASE-1 IN COMPLEX WITH HEME; SELELENO-METHIONINE DERIVATIVE, MUTATED AT M51T,M93L,M155L,M191L. | ||||||
Components | HEME OXYGENASE-1Heme oxygenase | ||||||
Keywords | OXIDOREDUCTASE / ALL ALPHA / PROTEIN-SUBSTRATE 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 nutrient / cellular response to arsenic-containing substance / 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 / Resolution: 2.2 Å | ||||||
Authors | Sugishima, M. / Omata, Y. / Kakuta, Y. / Sakamoto, H. / Noguchi, M. / Fukuyama, K. | ||||||
Citation | Journal: FEBS Lett. / Year: 2000 Title: Crystal structure of rat heme oxygenase-1 in complex with heme. Authors: Sugishima, M. / Omata, Y. / Kakuta, Y. / Sakamoto, H. / 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 | 1dvg.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dvg.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dvg ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dvg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30655.773 Da / Num. of mol.: 2 Mutation: M1(MSE), M9(MSE), M34(MSE), M51T, M93L, M155L, M186(MSE), M191L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: EXPRESSED AS RESIDUES 1-267 / Plasmid: PBACE / Production host: Escherichia coli (E. coli) / Strain (production host): PLK-F References: UniProt: P06762, heme oxygenase (biliverdin-producing) #2: Chemical | #3: 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: 2.3 Å3/Da / Density % sol: 46.52 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, TRIS-HCL, SODIUM ACETATE, CRYO:ADD GLYCEROL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7 Details: Omata, Y., (1998) Acta Crystallogr., Sect.D, 54, 1017. | ||||||||||||||||||||||||||||||
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: 0.9793 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 2, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.48 Å / Num. all: 27994 / Num. obs: 26622 / % possible obs: 95.1 % / Observed criterion σ(I): 1 / Redundancy: 2.62 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.28 % / Rmerge(I) obs: 0.227 / Num. unique all: 2492 / % possible all: 89.8 |
Reflection | *PLUS Num. measured all: 69625 |
Reflection shell | *PLUS % possible obs: 89.8 % |
-Processing
Software |
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Refinement | Resolution: 2.2→19.48 Å / σ(F): 0 / σ(I): 1
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Refinement step | Cycle: LAST / Resolution: 2.2→19.48 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.212 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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