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Yorodumi- PDB-5c8l: Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c8l | ||||||
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Title | Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase | ||||||
Components | NudF protein | ||||||
Keywords | HYDROLASE / Nudix | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bdellovibrio bacteriovorus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Gabelli, S.B. / de la Pena, A.H. / Suarez, A. / Amzel, L.M. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. Authors: de la Pena, A.H. / Suarez, A. / Duong-Ly, K.C. / Schoeffield, A.J. / Pizarro-Dupuy, M.A. / Zarr, M. / Pineiro, S.A. / Amzel, L.M. / Gabelli, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c8l.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c8l.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 5c8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/5c8l ftp://data.pdbj.org/pub/pdb/validation_reports/c8/5c8l | HTTPS FTP |
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-Related structure data
Related structure data | 5c7qSC 5c7tC 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
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 21290.469 Da / Num. of mol.: 2 / Mutation: E140Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: nudF, Bd3179 / Plasmid: pET24 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q6MIH8, ADP-ribose diphosphatase #2: Sugar | |
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-Non-polymers , 4 types, 331 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.75-2.0 M ammonium sulfate, 0.1 M HEPES pH 7.0, and 0-0.5% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.541 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 24, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 35689 / % possible obs: 92.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.064 / Χ2: 2.694 / Net I/av σ(I): 42.841 / Net I/σ(I): 19.1 / Num. measured all: 201670 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5C7Q Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2048 / WRfactor Rwork: 0.16 / FOM work R set: 0.8594 / SU B: 2.697 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1291 / SU Rfree: 0.1249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.11 Å2 / Biso mean: 28.662 Å2 / Biso min: 15.95 Å2
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Refinement step | Cycle: final / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.798→1.845 Å / Total num. of bins used: 20
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