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Yorodumi- PDB-1ni6: Comparisions of the Heme-Free and-Bound Crystal Structures of Hum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ni6 | |||||||||
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Title | Comparisions of the Heme-Free and-Bound Crystal Structures of Human Heme Oxygenase-1 | |||||||||
Components | Heme oxygenase 1HMOX1 | |||||||||
Keywords | OXYGEN STORAGE/TRANSPORT / heme oxygenase-1 / heme degradation / OXYGEN STORAGE-TRANSPORT COMPLEX | |||||||||
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: 2.1 Å | |||||||||
Authors | Lad, L. / Schuller, D.J. / Friedman, J. / Li, H. / Shimizu, 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ni6.cif.gz | 192.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ni6.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ni6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/1ni6 ftp://data.pdbj.org/pub/pdb/validation_reports/ni/1ni6 | HTTPS FTP |
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-Related structure data
Related structure data | 1n3uC 1n45C 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25925.568 Da / Num. of mol.: 4 / Fragment: apo form Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HMOX1 / Plasmid: pCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha References: UniProt: P09601, heme oxygenase (biliverdin-producing) #2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose / | #3: Chemical | ChemComp-CL / | #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: 2.18 Å3/Da / Density % sol: 43.46 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: ammonium sulphate, 1,6 hexane diol, HEPES, water, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 301K |
-Data collection
Diffraction | Mean temperature: 119 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 17, 2001 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 52492 / Num. obs: 49421 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.049 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.67 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.02 / Num. unique all: 2309 / Rsym value: 0.49 / % possible all: 87.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QQ8 1qq8 Resolution: 2.1→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 46.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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