+Open data
-Basic information
Entry | Database: PDB / ID: 1irm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of apo heme oxygenase-1 | ||||||
Components | apo heme oxygenase-1 | ||||||
Keywords | OXIDOREDUCTASE / disordered alpha helix / apo form of hemoprotein | ||||||
Function / homology | Function and homology information Regulation of HMOX1 expression and activity / arachidonate omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / cellular response to cisplatin ...Regulation of HMOX1 expression and activity / arachidonate omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / response to arachidonate / heme metabolic process / cellular response to cisplatin / heme oxygenase (biliverdin-producing) / heme oxidation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / heme oxygenase (decyclizing) activity / phospholipase D activity / wound healing involved in inflammatory response / negative regulation of muscle cell apoptotic process / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of mast cell cytokine production / heme catabolic process / cellular response to arsenic-containing substance / negative regulation of epithelial cell apoptotic process / cellular response to nutrient / positive regulation of epithelial cell apoptotic process / erythrocyte homeostasis / negative regulation of ferroptosis / epithelial cell apoptotic process / positive regulation of cell migration involved in sprouting angiogenesis / small GTPase-mediated signal transduction / negative regulation of macroautophagy / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / phospholipid metabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to cadmium ion / response to nicotine / liver regeneration / macroautophagy / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / response to hydrogen peroxide / caveola / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / response to estrogen / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / cellular response to heat / angiogenesis / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / response to oxidative stress / response to hypoxia / intracellular signal transduction / response to xenobiotic stimulus / negative regulation of cell population proliferation / 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 / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Sugishima, M. / Sakamoto, H. / Kakuta, Y. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal structure of rat apo-heme oxygenase-1 (HO-1): mechanism of heme binding in HO-1 inferred from structural comparison of the apo and heme complex forms Authors: Sugishima, M. / Sakamoto, H. / Kakuta, Y. / Omata, Y. / Hayashi, S. / Noguchi, M. / Fukuyama, K. #1: Journal: FEBS Lett. / Year: 2000 Title: Crystal Structure of rat heme oxygenase-1 in complex with heme Authors: Sugishima, M. / Omata, Y. / Kakuta, Y. / Sakamoto, H. / Noguchi, M. / Fukuyama, K. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and preliminary X-ray diffraction studies on the water soluble form of rat heme oxygenase-1 in complex with heme Authors: Omata, Y. / Asada, S. / Sakamoto, H. / Fukuyama, K. / Noguchi, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1irm.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1irm.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 1irm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1irm_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1irm_full_validation.pdf.gz | 505.8 KB | Display | |
Data in XML | 1irm_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 1irm_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/1irm ftp://data.pdbj.org/pub/pdb/validation_reports/ir/1irm | HTTPS FTP |
-Related structure data
Related structure data | 1dveS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30612.496 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pBAce / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P06762, heme oxygenase (biliverdin-producing) #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.45 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, PEG400, HEPES, stronthium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.709 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 24, 2000 |
Radiation | Monochromator: Si(111) double monochrometor / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.709 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→46.625 Å / Num. all: 25283 / Num. obs: 25283 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.06 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3692 / Rsym value: 0.25 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 93875 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.25 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DVE Resolution: 2.55→46.625 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: To solve the structure of merohedral twinning crystal, LSQ refinement target used as ( Fo - k( sqrt 0.55Fc^2 + 0.45Fc'^2] ) )^2
| ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.47 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→46.625 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.307 / Rfactor Rwork: 0.202 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.3853 / Rfactor Rwork: 0.322 |