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Yorodumi- PDB-6k36: Crystal structure of BioU from Synechocystis sp.PCC6803 conjugate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k36 | ||||||
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Title | Crystal structure of BioU from Synechocystis sp.PCC6803 conjugated with DAPA | ||||||
Components | Slr0355 protein | ||||||
Keywords | OXIDOREDUCTASE / BioU / biotin biosynthesis / dehydrogenase / cyanobacteria | ||||||
Function / homology | Function and homology information 8-amino-7-oxononanoate carboxylating dehydrogenase / biotin biosynthetic process / amino acid metabolic process / transaminase activity / NAD binding / NADP binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Sakaki, K. / Tomita, T. / Nishiyama, M. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Authors: Sakaki, K. / Ohishi, K. / Shimizu, T. / Kobayashi, I. / Mori, N. / Matsuda, K. / Tomita, T. / Watanabe, H. / Tanaka, K. / Kuzuyama, T. / Nishiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k36.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k36.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 6k36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/6k36 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/6k36 | HTTPS FTP |
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-Related structure data
Related structure data | 6ir4C 6itdSC 6k37C 6k38C S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37852.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: slr0355 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55650 |
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#2: Chemical | ChemComp-CWF / ( |
#3: 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: 1.89 Å3/Da / Density % sol: 35.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% (w/v) PEG 3350, 0.2M potassium formate, 0.21M HEPES-NaOH (pH7.0) |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 13306 / % possible obs: 99.9 % / Redundancy: 8.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.031 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.604 / Num. unique obs: 642 / CC1/2: 0.88 / Rpim(I) all: 0.211 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ITD Resolution: 2.3→30.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.266 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.288 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.443 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→30.81 Å
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Refine LS restraints |
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