+Open data
-Basic information
Entry | Database: PDB / ID: 4eoe | ||||||
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Title | Crystal structure of H74A 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. PCC 6803 substr. Kazusa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Kabasakal, B.V. / Fisher, A.J. | ||||||
Citation | Journal: To be Published Title: Crystal structure of H74A synechocystis sp. pcya Authors: Kabasakal, B.V. / Gae, D.D. / 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 | 4eoe.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eoe.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 4eoe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/4eoe ftp://data.pdbj.org/pub/pdb/validation_reports/eo/4eoe | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 28089.086 Da / Num. of mol.: 1 / Mutation: H74A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC6803 / Gene: pcyA, slr0116 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase | ||
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#2: Chemical | ChemComp-BLA / | ||
#3: Chemical | #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: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1-1.25 M sodium citrate, 0.1-0.4 M NaCl in 0.1 M Tris HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→39 Å / Num. all: 88225 / Num. obs: 88225 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 12.12 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.029 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.2→1.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4616 / Rsym value: 0.305 / % possible all: 67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→39 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.997 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / 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: 7.862 Å2
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Refine analyze | Luzzati coordinate error obs: 0.036 Å / Luzzati sigma a obs: 0.036 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.18→1.211 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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