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Yorodumi- PDB-2bix: Crystal structure of apocarotenoid cleavage oxygenase from Synech... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bix | ||||||
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Title | Crystal structure of apocarotenoid cleavage oxygenase from Synechocystis, Fe-free apoenzyme | ||||||
Components | APOCAROTENOID-CLEAVING OXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / OXYGENASE / NON-HEME IRON / CAROTENOID CLEAVAGE / RETINAL FORMATION / DIOXYGENASE | ||||||
Function / homology | all-trans-8'-apo-beta-carotenal 15,15'-oxygenase / all-trans-8'-apo-beta-carotenal 15,15'-oxygenase activity / carotenoid dioxygenase activity / 9-cis-epoxycarotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / metal ion binding / Apocarotenoid-15,15'-oxygenase Function and homology information | ||||||
Biological species | SYNECHOCYSTIS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.68 Å | ||||||
Authors | Kloer, D.P. / Ruch, S. / Al-Babili, S. / Beyer, P. / Schulz, G.E. | ||||||
Citation | Journal: Science / Year: 2005 Title: The Structure of a Retinal-Forming Carotenoid Oxygenase Authors: Kloer, D.P. / Ruch, S. / Al-Babili, S. / Beyer, P. / Schulz, G.E. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bix.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bix.ent.gz | 158.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bix_validation.pdf.gz | 822.7 KB | Display | wwPDB validaton report |
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Full document | 2bix_full_validation.pdf.gz | 866.4 KB | Display | |
Data in XML | 2bix_validation.xml.gz | 41 KB | Display | |
Data in CIF | 2bix_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/2bix ftp://data.pdbj.org/pub/pdb/validation_reports/bi/2bix | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.35963, -0.20798, 0.90962), Vector: |
-Components
#1: Protein | Mass: 54344.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC 6803 / Plasmid: PET3B-ACO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P74334 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE NAME OF THE MOLECULE IN THE UNIPROT DATABASE WITH ACCESSION NUMBER P74334 IS LIGNOSTILBENE- ...THE NAME OF THE MOLECULE IN THE UNIPROT DATABASE WITH ACCESSION NUMBER P74334 IS LIGNOSTILB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.57 % |
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Crystal grow | pH: 5.7 / Details: pH 5.70 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0716 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0716 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→45.8 Å / Num. obs: 44859 / % possible obs: 98.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.68→2.85 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 7.2 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.68→47.14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET MODEL WITH MASK / Bsol: 188 Å2 / ksol: 0.92 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→47.14 Å
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Refine LS restraints |
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