[English] 日本語
![](img/lk-miru.gif)
- PDB-1ni6: Comparisions of the Heme-Free and-Bound Crystal Structures of Hum... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ni6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Comparisions of the Heme-Free and-Bound Crystal Structures of Human Heme Oxygenase-1 | |||||||||
![]() | Heme oxygenase 1 | |||||||||
![]() | OXYGEN STORAGE/TRANSPORT / heme oxygenase-1 / heme degradation / OXYGEN STORAGE-TRANSPORT COMPLEX | |||||||||
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 / erythrocyte homeostasis / endothelial cell proliferation / epithelial cell apoptotic process / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of macroautophagy / The NLRP3 inflammasome / positive regulation of macroautophagy / 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 / negative regulation of smooth muscle cell proliferation / 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 / angiogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / mitochondrial outer membrane / response to oxidative stress / 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. / Schuller, D.J. / Friedman, J. / Li, H. / Shimizu, H. / Ortiz de Montellano, P.R. / Poulos, T.L. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 192.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 153.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 488.2 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n3uC ![]() 1n45C ![]() 1qq8 S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
3 | ![]()
| ||||||||||
4 | ![]()
| ||||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.46 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|