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Yorodumi- PDB-7ykb: Neutron Structure of PcyA D105N Mutant Complexed with Biliverdin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ykb | ||||||
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Title | Neutron Structure of PcyA D105N Mutant Complexed with Biliverdin at Room Temperature | ||||||
Components | Phycocyanobilin:ferredoxin oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / phycocyanobilin / ferredoxin oxi-doreductase / neutron / hydrogen / proton / mutant / reaction / absorption spectrum | ||||||
Function / homology | phycocyanobilin:ferredoxin oxidoreductase / phycocyanobilin:ferredoxin oxidoreductase activity / Phycocyanobilin:ferredoxin oxidoreductase / Ferredoxin-dependent bilin reductase / Ferredoxin-dependent bilin reductase / phytochromobilin biosynthetic process / cobalt ion binding / Chem-BLR / Phycocyanobilin:ferredoxin oxidoreductase Function and homology information | ||||||
Biological species | Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Unno, M. / Nanasawa, R. | ||||||
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 | 7ykb.cif.gz | 161.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ykb.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ykb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/7ykb ftp://data.pdbj.org/pub/pdb/validation_reports/yk/7ykb | HTTPS FTP |
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-Related structure data
Related structure data | 7yk9C 3f0mS C: citing same article (ref.) S: Starting model for refinement |
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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: 28155.172 Da / Num. of mol.: 1 / Mutation: D105N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: Kazusa / Gene: pcyA / Production host: Escherichia coli (E. coli) References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase |
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#2: Chemical | ChemComp-BLR / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: NaCl, ammonium sulfate, MES |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Biso Wilson estimate: 15.07 Å2 / Entry-ID: 7YKB
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Reflection shell |
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-Processing
Software |
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Refinement | SU ML: 0.1322 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 17.9555 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 3F0M / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL
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Refinement step | Cycle: LAST / Resolution: 1.38→34.58 Å
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Refine LS restraints |
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LS refinement shell |
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