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Yorodumi- PDB-6btd: Crystal structure of deoxyribose-phosphate aldolase from Bacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6btd | ||||||
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Title | Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose | ||||||
Components | Fuculose phosphate aldolase | ||||||
Keywords | LYASE / 5-deoxyribose / radical SAM enzyme byproduct / aldolase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å | ||||||
Authors | Li, Q. / Bruner, S.D. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Salvage of the 5-deoxyribose byproduct of radical SAM enzymes. Authors: Beaudoin, G.A.W. / Li, Q. / Folz, J. / Fiehn, O. / Goodsell, J.L. / Angerhofer, A. / Bruner, S.D. / Hanson, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6btd.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6btd.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 6btd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6btd_validation.pdf.gz | 430.6 KB | Display | wwPDB validaton report |
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Full document | 6btd_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 6btd_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 6btd_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/6btd ftp://data.pdbj.org/pub/pdb/validation_reports/bt/6btd | HTTPS FTP |
-Related structure data
Related structure data | 6btgC 4c24S 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: 24943.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: BK775_23715, CCZ40_07290 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: A0A231I520, L-fuculose-phosphate aldolase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-MN / |
#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: 2.63 Å3/Da / Density % sol: 53.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 200 mM NaCl, 25 % (v/v) PEG-3350, 100 mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→35.55 Å / Num. obs: 39118 / % possible obs: 99.93 % / Redundancy: 28.7 % / CC1/2: 1 / Rmerge(I) obs: 0.06302 / Rrim(I) all: 0.06417 / Net I/σ(I): 41.73 |
Reflection shell | Resolution: 1.551→1.606 Å / Redundancy: 28.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 7.37 / Num. unique obs: 3800 / CC1/2: 0.973 / Rrim(I) all: 0.06417 / % possible all: 99.29 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C24 Resolution: 1.551→35.547 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.551→35.547 Å
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Refine LS restraints |
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LS refinement shell |
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