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Yorodumi- PDB-2x9o: STRUCTURE OF 15, 16- DIHYDROBILIVERDIN:FERREDOXIN OXIDOREDUCTASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x9o | ||||||
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Title | STRUCTURE OF 15, 16- DIHYDROBILIVERDIN:FERREDOXIN OXIDOREDUCTASE (PebA) | ||||||
Components | 15,16-DIHYDROBILIVERDIN-FERREDOXIN OXIDOREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / PHYCOBILIN SYNTHESIS / CYANOBACTERIA / PHYCOERYTHROBILIN | ||||||
Function / homology | Function and homology information 15,16-dihydrobiliverdin:ferredoxin oxidoreductase / 15,16-dihydrobiliverdin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding Similarity search - Function | ||||||
Biological species | SYNECHOCOCCUS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | ||||||
Authors | Busch, A.W.U. / Frankenberg-Dinkel, N. / Hofmann, E. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Structural and Mechanistic Insight Into the Ferredoxin-Mediated Two-Electron Reduction of Bilins. Authors: Busch, A.W.U. / Reijerse, E.J. / Lubitz, W. / Frankenberg-Dinkel, N. / Hofmann, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x9o.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x9o.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 2x9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/2x9o ftp://data.pdbj.org/pub/pdb/validation_reports/x9/2x9o | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28137.084 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS SP. (bacteria) / Strain: WH8020 / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q02189, 15,16-dihydrobiliverdin:ferredoxin oxidoreductase |
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#2: Chemical | ChemComp-BLA / |
#3: Water | ChemComp-HOH / |
Sequence details | THE FIRST METHIONINE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 100MM HEPES PH 7.0, 25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978946 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978946 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40.18 Å / Num. obs: 33089 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.03 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.53 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.91 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.55→40.185 Å / SU ML: 0.17 / σ(F): 2 / Phase error: 21.61 / Stereochemistry target values: ML Details: RESIDUES 128 AND 129 WERE NOT MODELLED DUE TO MISSING DENSITY
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.321 Å2 / ksol: 0.343 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→40.185 Å
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Refine LS restraints |
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LS refinement shell |
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