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- PDB-1oze: Crystal Structures of the Ferric, Ferrous, and Ferrous-NO Forms o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oze | ||||||
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Title | Crystal Structures of the Ferric, Ferrous, and Ferrous-NO Forms of the Asp140Ala Mutant of Human Heme Oxygenase-1:Catalytic Implications | ||||||
![]() | Heme oxygenase 1 | ||||||
![]() | OXIDOREDUCTASE / heme oxygenase / heme degradation | ||||||
Function / homology | ![]() Regulation of HMOX1 expression and activity / heme oxygenase (biliverdin-producing) / low-density lipoprotein particle clearance / cellular response to cisplatin / heme oxidation / smooth muscle hyperplasia / heme oxygenase (decyclizing) activity / negative regulation of leukocyte migration / 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 / heme oxygenase (decyclizing) activity / negative regulation of leukocyte migration / 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 / endothelial cell proliferation / erythrocyte homeostasis / negative regulation of ferroptosis / epithelial cell apoptotic process / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of macroautophagy / positive regulation of cell migration involved in sprouting angiogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / macroautophagy / positive regulation of smooth muscle cell proliferation / negative regulation of smooth muscle cell proliferation / Iron uptake and transport / Heme signaling / response to nicotine / response to hydrogen peroxide / Cytoprotection by HMOX1 / multicellular organismal-level iron ion homeostasis / positive regulation of angiogenesis / cellular response to heat / 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 / structural molecule activity / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein homodimerization activity / extracellular space / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lad, L. / Wang, J. / Li, H. / Friedman, J. / Ortiz de Montellano, P.R. / Poulos, T.L. | ||||||
![]() | ![]() Title: Crystal structures of the ferric, ferrous, and ferrous-NO forms of the Asp140Ala mutant of human heme oxygenase-1: catalytic implications Authors: Lad, L. / Wang, J. / Li, H. / Friedman, J. / Bhaskar, B. / Ortiz de Montellano, P.R. / Poulos, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.4 KB | Display | ![]() |
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PDB format | ![]() | 80.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1oykC ![]() 1oylC ![]() 1ozlC ![]() 1ozrC ![]() 1ozwC ![]() 1qq8 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 26854.605 Da / Num. of mol.: 2 / Fragment: residues 1-233 of SWS P09601 / Mutation: Asp140ala Source method: isolated from a genetically manipulated source Details: Heme-complexed / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P09601, heme oxygenase (biliverdin-producing) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.22 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: ammomium sulphate, 1,6 hexanediol, HEPES, water, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 301K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 119 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 28, 2002 / 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: 2.19→50 Å / Num. all: 24350 / Num. obs: 24079 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.105 / Rsym value: 0.091 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 4.39 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 2.29 / Num. unique all: 2151 / Rsym value: 0.089 / % possible all: 94.1 |
Reflection | *PLUS Num. obs: 30463 / % possible obs: 95.1 % / Num. measured all: 157747 |
Reflection shell | *PLUS Rmerge(I) obs: 0.603 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QQ8 ![]() 1qq8 Resolution: 2.19→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: 2.19→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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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |