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Yorodumi- PDB-1we1: Crystal structure of heme oxygenase-1 from cyanobacterium Synecho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1we1 | ||||||
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Title | Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC6803 in complex with heme | ||||||
Components | Heme oxygenase 1 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information : / heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / photosynthesis / response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sugishima, M. / Migita, C.T. / Zhang, X. / Yoshida, T. / Fukuyama, K. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2004 Title: Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme Authors: Sugishima, M. / Migita, C.T. / Zhang, X. / Yoshida, T. / Fukuyama, K. #1: Journal: Eur.J.Biochem. / Year: 2003 Title: Expression and characterization of cyanobacterium heme oxygenase, a key enzyme in the phycobilin synthesis. Properties of the heme complex of recombinant active enzyme Authors: Migita, C.T. / Zhang, X. / Yoshida, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1we1.cif.gz | 194.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1we1.ent.gz | 155.8 KB | Display | PDB format |
PDBx/mmJSON format | 1we1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1we1_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1we1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1we1_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 1we1_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/1we1 ftp://data.pdbj.org/pub/pdb/validation_reports/we/1we1 | HTTPS FTP |
-Related structure data
Related structure data | 1dveS 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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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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Details | biological unit is monomer |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 27083.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P72849, heme oxygenase (biliverdin-producing) |
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-Non-polymers , 5 types, 228 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-IPA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: PEG 400, 2-propanol, 1,5-diaminopentane dihydrochloride, sodium citrate, pottasium phosphate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.5 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 29, 2004 |
Radiation | Monochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 46584 / Num. obs: 46584 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 61.6 Å2 / Rsym value: 0.064 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5929 / Rsym value: 0.302 / % possible all: 83.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DVE Resolution: 2.5→20 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: -0.079 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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