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- PDB-5b4i: Crystal structure of I86D mutant of phycocyanobilin:ferredoxin ox... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b4i | ||||||||||||||||||||||||
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Title | Crystal structure of I86D mutant of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin (data 2) | ||||||||||||||||||||||||
![]() | Phycocyanobilin:ferredoxin oxidoreductase | ||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / Photosynthesis pigment / heme metabolism | ||||||||||||||||||||||||
Function / homology | ![]() phycocyanobilin:ferredoxin oxidoreductase / phycocyanobilin:ferredoxin oxidoreductase activity / phytochromobilin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Hagiwara, Y. / Wada, K. / Irikawa, T. / Unno, M. / Fukuyama, K. / Sugishima, M. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin Authors: Hagiwara, Y. / Wada, K. / Irikawa, T. / Sato, H. / Unno, M. / Yamamoto, K. / Fukuyama, K. / Sugishima, M. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.2 KB | Display | ![]() |
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PDB format | ![]() | 104.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 793 KB | Display | ![]() |
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Full document | ![]() | 800.3 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b4hC ![]() 5b4jC ![]() 4qcdS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28158.086 Da / Num. of mol.: 1 / Mutation: I86D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase |
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#2: Chemical | ChemComp-BLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 53.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: sodium citrate, sodium chloride, Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→56.94 Å / Num. obs: 114063 / % possible obs: 99.3 % / Redundancy: 6 % / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.1→1.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.363 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QCD Resolution: 1.11→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 39 / Occupancy sum non hydrogen: 2304.9 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.11→10 Å
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Refine LS restraints |
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