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Yorodumi- PDB-6k37: Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 i... -
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-Basic information
Entry | Database: PDB / ID: 6k37 | ||||||
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Title | Crystal structure of BioU (K124A) from Synechocystis sp.PCC6803 in complex with NAD+ and the analog of reaction intermediate, 3-(1-aminoethyl)-nonanedioic acid | ||||||
Components | Slr0355 protein | ||||||
Keywords | OXIDOREDUCTASE / BioU / biotin biosynthesis / dehydrogenase / Synechocystis | ||||||
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: 2.5 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 | 6k37.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k37.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 6k37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k37_validation.pdf.gz | 890.5 KB | Display | wwPDB validaton report |
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Full document | 6k37_full_validation.pdf.gz | 905.7 KB | Display | |
Data in XML | 6k37_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 6k37_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/6k37 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/6k37 | HTTPS FTP |
-Related structure data
Related structure data | 6ir4C 6itdSC 6k36C 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
#1: Protein | Mass: 37794.789 Da / Num. of mol.: 1 / Mutation: K124A 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-NAD / |
#3: Chemical | ChemComp-CWL / ( |
#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: 1.87 Å3/Da / Density % sol: 34.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 28% PEG 3350, 0.2M Ammonium formate, 0.1M HEPES-NaOH (pH7.0), 5mM 3-(1-aminoethyl)-nonanedioic acid, 5mM NAD+ |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 10264 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.034 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.646 / Num. unique obs: 541 / CC1/2: 0.901 / Rpim(I) all: 0.212 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ITD Resolution: 2.5→38.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.505 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R Free: 0.347 / 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: 54.314 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→38.41 Å
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Refine LS restraints |
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