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Open data
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Basic information
Entry | Database: PDB / ID: 4wd4 | ||||||
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Title | Crystal structure of human HO1 H25R | ||||||
![]() | Heme oxygenase 1![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
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 / negative regulation of leukocyte migration / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caaveiro, J.M.M. / Morante, K. / Sigala, P. / Tsumoto, K. | ||||||
![]() | ![]() Title: In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis Authors: Sigala, P.A. / Morante, K. / Tsumoto, K. / Caaveiro, J.M. / Goldberg, D.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.3 KB | Display | ![]() |
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PDB format | ![]() | 152.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5btqC ![]() 1n45S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 10 - 223 / Label seq-ID: 14 - 227
NCS ensembles :
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Components
#1: Protein | ![]() Mass: 33293.074 Da / Num. of mol.: 4 / Mutation: H29R Source method: isolated from a genetically manipulated source Details: Mutation H25R First four residues do not belong to the sequence of HO1 (trombin cleavage site, and cloning artifact). Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P09601, heme oxygenase (biliverdin-producing) #2: Chemical | ChemComp-HEM / ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.69 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 100 mM HEPES, pH 7.4; 2.1 M (NH4)2SO4; 0.9% 1,6-hexane-diol; BIG_CHAP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.95→74.1 Å / Num. obs: 20111 / % possible obs: 97.4 % / Redundancy: 6.6 % / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2 / % possible all: 92.4 |
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Processing
Software | Name: REFMAC / Version: 5.8.0073 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() ![]() Starting model: 1N45 Resolution: 2.95→70.1 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.885 / SU B: 22.227 / SU ML: 0.39 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.051 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→70.1 Å
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Refine LS restraints |
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