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- PDB-1p3u: Crystal Structures of the NO-and CO-Bound Heme Oxygenase From Nei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p3u | ||||||
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Title | Crystal Structures of the NO-and CO-Bound Heme Oxygenase From Neisseria Meningitidis: Implications for Oxygen Activation | ||||||
![]() | Heme oxygenase 1 | ||||||
![]() | OXIDOREDUCTASE / heme oxygenase / heme degradation | ||||||
Function / homology | ![]() heme oxidation / heme oxygenase (decyclizing) activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Friedman, J. / Lad, L. / Deshmukh, R. / Li, H. / Wilks, A. / Poulos, T.L. | ||||||
![]() | ![]() Title: Crystal structures of the NO- and CO-bound heme oxygenase from Neisseriae meningitidis. Implications for O2 activation Authors: Friedman, J. / Lad, L. / Deshmukh, R. / Li, H. / Wilks, A. / Poulos, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59 KB | Display | ![]() |
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PDB format | ![]() | 41.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474 KB | Display | ![]() |
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Full document | ![]() | 477.5 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p3tC ![]() 1p3vC ![]() 1j77S C: citing same article ( 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: 23609.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Heme-complexed / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9RGD9, heme oxygenase (biliverdin-producing) |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.14 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: tris-HCl, sodium acetate, PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 119 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 21237 / Num. obs: 20581 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.035 / Rsym value: 0.034 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1922 / Rsym value: 0.556 / % possible all: 97.8 |
Reflection | *PLUS Num. obs: 34991 / % possible obs: 86.9 % / Num. measured all: 85041 |
Reflection shell | *PLUS % possible obs: 90.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J77 Resolution: 1.75→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |