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Yorodumi- PDB-3tgm: X-Ray Crystal Structure of Human Heme Oxygenase-1 in Complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tgm | ||||||
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Title | X-Ray Crystal Structure of Human Heme Oxygenase-1 in Complex with 1-(1H-imidazol-1-yl)-4,4-diphenyl-2 butanone | ||||||
Components | Heme oxygenase 1HMOX1 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Alpha helix / oxidoreductase / heme / microsomes / oxidoreductase-oxidoreductase inhibitor 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å | ||||||
Authors | Rahman, M.N. / Jia, Z. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: A novel, "double-clamp" binding mode for human heme oxygenase-1 inhibition. Authors: Rahman, M.N. / Vlahakis, J.Z. / Vukomanovic, D. / Lee, W. / Szarek, W.A. / Nakatsu, K. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tgm.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tgm.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 3tgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/3tgm ftp://data.pdbj.org/pub/pdb/validation_reports/tg/3tgm | HTTPS FTP |
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-Related structure data
Related structure data | 1n3uS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-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, HO, 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: Chemical | ChemComp-HEZ / | #5: 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: 2.12 Å3/Da / Density % sol: 41.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES (pH 7.5), 2.2 M ammonium sulfate, 0.95% 1,6-hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 4, 2011 / Details: 3.3 Undulator (Undulator A) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→20 Å / Num. obs: 11070 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.63 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N3U Chain A Resolution: 2.85→19.82 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.993 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.859 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.923 Å / Total num. of bins used: 20
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