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Yorodumi- PDB-1j77: Crystal Structure of Gram-negative Bacterial Heme Oxygenase Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j77 | ||||||
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Title | Crystal Structure of Gram-negative Bacterial Heme Oxygenase Complexed with Heme | ||||||
Components | HemO | ||||||
Keywords | OXIDOREDUCTASE / proximal histidine / distal helix | ||||||
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 / MAD / Resolution: 1.5 Å | ||||||
Authors | Schuller, D.J. / Zhu, W. / Stojiljkovic, I. / Wilks, A. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structure of heme oxygenase from the gram-negative pathogen Neisseria meningitidis and a comparison with mammalian heme oxygenase-1. Authors: Schuller, D.J. / Zhu, W. / Stojiljkovic, I. / 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 | 1j77.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j77.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j77_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1j77_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1j77_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 1j77_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j77 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j77 | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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Details | the enzyme is a monomer |
-Components
#1: Protein | Mass: 23609.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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: 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: 2.12 Å3/Da / Density % sol: 43 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 3350, sodium acetate, Tris hydrochloride, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.5498, 1.7377, 1.7401, 1.9075 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 2000 Details: Flat mirror(vertical) single crystal (Si311) bent monochromator (horizontal) | |||||||||||||||
Radiation | Monochromator: bent crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→44.67 Å / Num. all: 31486 / Num. obs: 31486 / % possible obs: 0.946 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 23.743 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 13.3 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1381 / % possible all: 92.1 | |||||||||||||||
Reflection | *PLUS % possible obs: 94.9 % / Num. measured all: 161249 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 92.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→53.45 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: REFMAC5 / Details: Maximum likelihood based on F
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Displacement parameters | Biso mean: 22.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→53.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: -0
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Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor Rfree: 0.26 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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