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Yorodumi- PDB-1p3u: Crystal Structures of the NO-and CO-Bound Heme Oxygenase From Nei... -
+Open data
-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 | ||||||
Components | Heme oxygenase 1HMOX1 | ||||||
Keywords | OXIDOREDUCTASE / heme oxygenase / heme degradation | ||||||
Function / homology | Function and homology information heme oxidation / heme oxygenase (decyclizing) activity / metal ion binding Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Friedman, J. / Lad, L. / Deshmukh, R. / Li, H. / Wilks, A. / Poulos, T.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p3u.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p3u.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 1p3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/1p3u ftp://data.pdbj.org/pub/pdb/validation_reports/p3/1p3u | HTTPS FTP |
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-Related structure data
Related structure data | 1p3tC 1p3vC 1j77S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Neisseria meningitidis (bacteria) / Gene: hemO / Plasmid: pWMZ1651 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |