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Yorodumi- PDB-4g99: Rat Heme Oxygenase-1 in complex with Heme and CO at 100 K after w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g99 | ||||||
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Title | Rat Heme Oxygenase-1 in complex with Heme and CO at 100 K after warming to 160 K | ||||||
Components | Heme oxygenase 1HMOX1 | ||||||
Keywords | OXIDOREDUCTASE / ALL ALPHA PROTEIN / OXYGENASE | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Sugishima, M. / Moffat, K. / Noguchi, M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Discrimination between CO and O(2) in heme oxygenase: comparison of static structures and dynamic conformation changes following CO photolysis. Authors: Sugishima, M. / Moffat, K. / Noguchi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g99.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g99.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 4g99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/4g99 ftp://data.pdbj.org/pub/pdb/validation_reports/g9/4g99 | HTTPS FTP |
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-Related structure data
Related structure data | 4g7lC 4g7pC 4g7tC 4g7uC 4g8pC 4g8uC 4g8wC 4g98SC C: citing same article (ref.) 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: UNP residues 1-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hmox1 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P06762, heme oxygenase (biliverdin-producing) |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-CMO / |
#4: Chemical | ChemComp-FMT / |
#5: 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: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 4M sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2011 |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 13968 / Num. obs: 13968 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rsym value: 0.072 / Net I/σ(I): 11.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 4G98 Resolution: 2.3→32.97 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.414 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.933 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→32.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 Å / Total num. of bins used: 20
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