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- PDB-2zvu: Crystal structure of rat heme oxygenase-1 in complex with ferrous... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zvu | ||||||
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Title | Crystal structure of rat heme oxygenase-1 in complex with ferrous verdoheme | ||||||
![]() | Heme oxygenase 1![]() | ||||||
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Function / homology | ![]() Regulation of HMOX1 expression and activity / arachidonic acid omega-hydroxylase activity / Iron uptake and transport / response to 3-methylcholanthrene / Heme degradation / Cytoprotection by HMOX1 / negative regulation of mast cell degranulation / heme metabolic process / response to arachidonic acid / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sato, H. / Sugishima, M. / Fukuyama, K. / Noguchi, M. | ||||||
![]() | ![]() Title: Crystal structure of rat haem oxygenase-1 in complex with ferrous verdohaem: presence of a hydrogen-bond network on the distal side Authors: Sato, H. / Sugishima, M. / Sakamoto, H. / Higashimoto, Y. / Shimokawa, C. / Fukuyama, K. / Palmer, G. / Noguchi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.9 KB | Display | ![]() |
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PDB format | ![]() | 43.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ubbS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 30612.496 Da / Num. of mol.: 1 / Fragment: UNP residues 1-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P06762, heme oxygenase (biliverdin-producing) |
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#2: Chemical | ChemComp-VEA / |
#3: Chemical | ChemComp-FMT / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.19 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 4.0M sodium formate, 10mM sodium azide, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 28, 2008 |
Radiation | Monochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→50 Å / Num. all: 15541 / Num. obs: 15371 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1396 / % possible all: 90.7 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1UBB Resolution: 2.2→32.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.45 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.217 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.809 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→32.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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