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Yorodumi- PDB-1n3u: Crystal structure of human heme oxygenase 1 (HO-1) in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n3u | ||||||
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Title | Crystal structure of human heme oxygenase 1 (HO-1) in complex with its substrate heme, crystal form B | ||||||
Components | heme oxygenase 1HMOX1 | ||||||
Keywords | OXIDOREDUCTASE / alpha helices / heme-binding site | ||||||
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: 2.58 Å | ||||||
Authors | Lad, L. / Schuller, D.J. / Friedman, J.P. / Li, H. / Ortiz de Montellano, P.R. / Poulos, T.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Comparison of the heme-free and -bound crystal structures of human heme oxygenase-1 Authors: Lad, L. / Schuller, D.J. / Shimizu, H. / Friedman, J. / Li, H. / Ortiz de Montellano, P.R. / Poulos, T.L. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal Structure of Human Heme Oxygenase-1 Authors: Schuller, D.J. / Wilks, A. / Ortiz de Montellano, P.R. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n3u.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n3u.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 1n3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n3u ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n3u | HTTPS FTP |
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-Related structure data
Related structure data | 1n45C 1ni6C 1qq8 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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2 |
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Unit cell |
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Details | the enzyme is a monomer |
-Components
#1: Protein | Mass: 26898.615 Da / Num. of mol.: 2 / Fragment: Residues 1-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1, HO1 / Plasmid: delta233-hHO-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha References: UniProt: P09601, heme oxygenase (biliverdin-producing) #2: Chemical | #3: Chemical | #4: 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: 2.31 Å3/Da / Density % sol: 46.28 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: ammonium sulfate, HEPES, 1,6-hexanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 301K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 28 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 1998 / Details: mirrors |
Radiation | Monochromator: mirrors + nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→78 Å / Num. all: 14937 / Num. obs: 14295 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 64.6 Å2 / Rsym value: 0.074 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.58→2.64 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3 / Num. unique all: 674 / Rsym value: 0.566 / % possible all: 94.4 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 78 Å / Num. obs: 14273 / Num. measured all: 100842 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / % possible obs: 94.4 % / Rmerge(I) obs: 0.566 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1QQ8 1qq8 Resolution: 2.58→70 Å / Isotropic thermal model: isotropic / Cross valid method: througout / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.58→70 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.6 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |