+Open data
-Basic information
Entry | Database: PDB / ID: 3nb8 | |||||||||
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Title | Crystal structure of oxidized H88Q Synechocystis sp. PCYA | |||||||||
Components | Phycocyanobilin:ferredoxin oxidoreductase | |||||||||
Keywords | OXIDOREDUCTASE / alpha-beta-alpha sandwich / radical chemistry | |||||||||
Function / homology | Function and homology information phycocyanobilin:ferredoxin oxidoreductase / phycocyanobilin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Gae, D.D. | |||||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants. Authors: Kohler, A.C. / Gae, D.D. / Richley, M.A. / Stoll, S. / Gunn, A. / Lim, S. / Martin, S.S. / Doukov, T.I. / Britt, R.D. / Ames, J.B. / Lagarias, J.C. / Fisher, A.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nb8.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nb8.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 3nb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/3nb8 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/3nb8 | HTTPS FTP |
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-Related structure data
Related structure data | 3f0lC 3f0mC 3nb9C 2d1eS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 28146.137 Da / Num. of mol.: 1 / Mutation: H88Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: pcyA, slr0116 / Production host: Escherichia coli (E. coli) References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-BLA / | #4: 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: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.7-2.2 M ammonium sulfate, 0.26-0.32 M NaCl, and 0.1 M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2007 |
Radiation | Monochromator: NI MIRROR + NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→26.21 Å / Num. all: 72052 / Num. obs: 64740 / % possible obs: 89.84 % |
Reflection shell | Resolution: 1.3→1.334 Å / % possible all: 78.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D1E Resolution: 1.3→26.21 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.381 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R Free: 0.053 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.215 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→26.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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