[English] 日本語
Yorodumi- PDB-1t5p: Human Heme Oxygenase Oxidation of alpha- and gamma-meso-phenylhemes -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t5p | ||||||
---|---|---|---|---|---|---|---|
Title | Human Heme Oxygenase Oxidation of alpha- and gamma-meso-phenylhemes | ||||||
Components | Heme oxygenase 1HMOX1 | ||||||
Keywords | OXIDOREDUCTASE / heme oxygenase / heme degredation | ||||||
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 / endothelial cell proliferation / erythrocyte homeostasis / positive regulation of epithelial cell apoptotic process / 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 / response to nicotine / negative regulation of smooth muscle cell proliferation / macroautophagy / Iron uptake and transport / positive regulation of smooth muscle cell proliferation / 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 / angiogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / response to oxidative stress / intracellular iron ion homeostasis / 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: 2.11 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1t5p.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1t5p.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 1t5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/1t5p ftp://data.pdbj.org/pub/pdb/validation_reports/t5/1t5p | HTTPS FTP |
---|
-Related structure data
Related structure data | 1s13C 1qq8 S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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, HO1, 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.8 % |
---|---|
Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: NH4SO4, hepes, hexanediol, Jeffamine-600 and water, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K |
-Data collection
Diffraction | Mean temperature: 119 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 2, 2004 / 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: 2.11→50 Å / Num. all: 23540 / Num. obs: 21619 / % possible obs: 91.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Rmerge(I) obs: 0.065 / Rsym value: 0.054 / Net I/σ(I): 21.2 |
Reflection shell | Highest resolution: 2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.039 / Mean I/σ(I) obs: 2.12 / Num. unique all: 2500 / Rsym value: 0.047 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qq8 1qq8 Resolution: 2.11→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→50 Å
| ||||||||||||||||||||
Refine LS restraints |
|