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- PDB-5btq: Crystal structure of human heme oxygenase 1 H25R with biliverdin bound -
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Open data
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Basic information
Entry | Database: PDB / ID: 5btq | ||||||
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Title | Crystal structure of human heme oxygenase 1 H25R with biliverdin bound | ||||||
![]() | Heme oxygenase 1![]() | ||||||
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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 | ![]() | 107 KB | Display | ![]() |
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PDB format | ![]() | 81.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wd4C ![]() 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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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 11 - 222 / Label seq-ID: 15 - 226
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Components
#1: Protein | ![]() Mass: 27331.133 Da / Num. of mol.: 2 / Fragment: UNP residues 1-233 / Mutation: H29R Source method: isolated from a genetically manipulated source Details: Mutation H25R / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P09601, heme oxygenase (biliverdin-producing) #2: Chemical | #3: Chemical | ChemComp-SO4 / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.35 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 100mM HEPES 2.1M Ammonium sulfate 0.9% 1,6-hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.08→43.5 Å / Num. obs: 26949 / % possible obs: 93.3 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.08→2.19 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.5 / % possible all: 75.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1N45 Resolution: 2.08→43.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.444 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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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: 30.208 Å2
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Refinement step | Cycle: 1 / Resolution: 2.08→43.5 Å
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Refine LS restraints |
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