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Yorodumi- PDB-7yk9: Neutron Structure of PcyA I86D Mutant Complexed with Biliverdin a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yk9 | ||||||
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Title | Neutron Structure of PcyA I86D Mutant Complexed with Biliverdin at Room Temperature | ||||||
Components | Phycocyanobilin:ferredoxin oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / phycocyanobilin / biliverdin / neutron / joint-refinement / room temperature / pigment / substrate / inactive / absorption spectrum / hydrogen atom / proton / mutant | ||||||
Function / homology | Function and homology information phycocyanobilin:ferredoxin oxidoreductase / phycocyanobilin:ferredoxin oxidoreductase activity / phytochromobilin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding Similarity search - Function | ||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Unno, M. / Igarashi, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states. Authors: Joutsuka, T. / Nanasawa, R. / Igarashi, K. / Horie, K. / Sugishima, M. / Hagiwara, Y. / Wada, K. / Fukuyama, K. / Yano, N. / Mori, S. / Ostermann, A. / Kusaka, K. / Unno, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yk9.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yk9.ent.gz | 104.6 KB | Display | PDB format |
PDBx/mmJSON format | 7yk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yk9_validation.pdf.gz | 488.1 KB | Display | wwPDB validaton report |
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Full document | 7yk9_full_validation.pdf.gz | 490.6 KB | Display | |
Data in XML | 7yk9_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 7yk9_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/7yk9 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/7yk9 | HTTPS FTP |
-Related structure data
Related structure data | 7ykbC 5b4hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Gene: pcyA / Production host: Escherichia coli (E. coli) References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase |
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#2: Chemical | ChemComp-BLR / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: ammonium sulfate, sodium chloride, sodium cacodylate |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Biso Wilson estimate: 26.18 Å2 / Entry-ID: 7YK9
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Reflection shell |
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-Processing
Software |
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Refinement | SU ML: 0.1786 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 17.1496 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5B4H / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL
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Refinement step | Cycle: LAST / Resolution: 1.9→36.91 Å
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Refine LS restraints |
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LS refinement shell |
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