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Yorodumi- PDB-2biw: Crystal structure of apocarotenoid cleavage oxygenase from Synech... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2biw | ||||||
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Title | Crystal structure of apocarotenoid cleavage oxygenase from Synechocystis, native enzyme | ||||||
Components | APOCAROTENOID-CLEAVING OXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / OXYGENASE / NON-HEME IRON / CAROTENOID CLEAVAGE / RETINAL FORMATION / DIOXYGENASE | ||||||
Function / homology | Function and homology information 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 / metal ion binding Similarity search - Function | ||||||
Biological species | SYNECHOCYSTIS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 | 2biw.cif.gz | 386.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2biw.ent.gz | 316.7 KB | Display | PDB format |
PDBx/mmJSON format | 2biw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2biw_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2biw_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2biw_validation.xml.gz | 77.8 KB | Display | |
Data in CIF | 2biw_validation.cif.gz | 104.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/2biw ftp://data.pdbj.org/pub/pdb/validation_reports/bi/2biw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 12 - 490 / Label seq-ID: 12 - 490
NCS oper:
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-Components
#1: Protein | Mass: 54344.191 Da / Num. of mol.: 4 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 | ChemComp-3ON / ( #3: Chemical | ChemComp-FE / #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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 66 % |
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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: 1.2399 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2399 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→44 Å / Num. obs: 111472 / % possible obs: 93.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.39→2.5 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 80.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ACO APO FORM Resolution: 2.39→44.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.241 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→44.41 Å
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Refine LS restraints |
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