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Yorodumi- PDB-1s13: Human Heme Oxygenase Oxidatition of alpha- and gamma-meso-Phenylhemes -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s13 | ||||||
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Title | Human Heme Oxygenase Oxidatition of alpha- and gamma-meso-Phenylhemes | ||||||
Components | Heme oxygenase 1HMOX1 | ||||||
Keywords | OXIDOREDUCTASE / heme oxygenase-1 / heme degradation | ||||||
Function / homology | Function and homology information Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxidation / smooth muscle hyperplasia / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxidation / smooth muscle hyperplasia / negative regulation of leukocyte migration / heme oxygenase (decyclizing) activity / wound healing involved in inflammatory response / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / heme catabolic process / cellular response to arsenic-containing substance / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / endothelial cell proliferation / Heme degradation / epithelial cell apoptotic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of macroautophagy / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of macroautophagy / The NLRP3 inflammasome / regulation of angiogenesis / Purinergic signaling in leishmaniasis infection / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of chemokine production / cellular response to cadmium ion / negative regulation of smooth muscle cell proliferation / macroautophagy / Iron uptake and transport / positive regulation of smooth muscle cell proliferation / response to nicotine / Heme signaling / response to hydrogen peroxide / Cytoprotection by HMOX1 / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / cellular response to hypoxia / Interleukin-4 and Interleukin-13 signaling / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / response to oxidative stress / mitochondrial outer membrane / intracellular signal transduction / 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 / extracellular space / nucleoplasm / membrane / identical protein binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Wang, J. / Niemevz, F. / Lad, L. / Buldain, G. / Poulos, T.L. / Ortiz de Montellano, P.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Human heme oxygenase oxidation of 5- and 15-phenylhemes. Authors: Wang, J. / Niemevz, F. / Lad, L. / Huang, L. / Alvarez, D.E. / Buldain, G. / Poulos, T.L. / Ortiz de Montellano, P.R. | ||||||
History |
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Remark 600 | heterogen The outer propionate is disordered in the ligand 2FH |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s13.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s13.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 1s13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/1s13 ftp://data.pdbj.org/pub/pdb/validation_reports/s1/1s13 | HTTPS FTP |
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-Related structure data
Related structure data | 1t5pC 1qq8 S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 26898.615 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1 or HO1 or HO / Plasmid: pCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha References: UniProt: P09601, 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: 2.08 Å3/Da / Density % sol: 40.87 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulphate, HEPES, hexanediol, jeffamine ED600, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K |
-Data collection
Diffraction | Mean temperature: 119 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 18, 2003 / Details: yale mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. all: 20845 / Num. obs: 20818 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.066 / Rsym value: 0.055 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.038 / Mean I/σ(I) obs: 2.12 / Num. unique all: 2477 / Rsym value: 0.046 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qq8 1qq8 Resolution: 2.29→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.29→50 Å
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Refine LS restraints |
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LS refinement shell |
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