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Yorodumi- PDB-1oyk: Crystal Structures of the Ferric, Ferrous, and Ferrous-NO Forms o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oyk | ||||||
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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 | ||||||
Components | Heme oxygenase 1 | ||||||
Keywords | OXIDOREDUCTASE / heme oxygenase / 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 / 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 / cellular response to cadmium ion / regulation of angiogenesis / Purinergic signaling in leishmaniasis infection / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of chemokine production / positive regulation of smooth muscle cell proliferation / negative regulation of smooth muscle cell proliferation / macroautophagy / 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 / positive regulation of canonical NF-kappaB signal transduction / cellular response to heat / Interleukin-4 and Interleukin-13 signaling / angiogenesis / intracellular iron ion homeostasis / response to oxidative stress / mitochondrial outer membrane / intracellular signal transduction / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / heme binding / perinuclear region of cytoplasm / enzyme binding / structural molecule activity / endoplasmic reticulum / protein homodimerization activity / extracellular space / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Lad, L. / Wang, J. / Li, H. / Friedman, J. / Ortiz de Montellano, P.R. / Poulos, T.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oyk.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oyk.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oyk_validation.pdf.gz | 541.3 KB | Display | wwPDB validaton report |
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Full document | 1oyk_full_validation.pdf.gz | 556 KB | Display | |
Data in XML | 1oyk_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1oyk_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/1oyk ftp://data.pdbj.org/pub/pdb/validation_reports/oy/1oyk | HTTPS FTP |
-Related structure data
Related structure data | 1oylC 1ozeC 1ozlC 1ozrC 1ozwC 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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-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.) 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: 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: 2.02 Å3/Da / Density % sol: 39.04 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: ammomium sulphate, 1,6 hexane-diol, 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 18, 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: 2.59→50 Å / Num. all: 33028 / Num. obs: 14071 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.071 / Rsym value: 0.066 / Net I/σ(I): 19.8 |
Reflection | *PLUS Num. obs: 33028 / Num. measured all: 135214 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.01 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QQ8 1qq8 Resolution: 2.59→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.59→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: 0.291 / Rfactor Rwork: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |