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Yorodumi- PDB-3bgk: The crystal structure of hypothetic protein SMU.573 from Streptoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bgk | ||||||
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Title | The crystal structure of hypothetic protein SMU.573 from Streptococcus mutans | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / alpha/beta three layer sandwich | ||||||
Function / homology | Function and homology information ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / nicotinamide nucleotide metabolic process / ATP binding Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / MAD / Resolution: 2.5 Å | ||||||
Authors | Liang, Y.H. / Zhou, Y.F. / Yang, C. / Su, X.D. | ||||||
Citation | Journal: To be Published Title: The crystal structure of Streptococcus mutans protein SMU.573 solved from the anomalous signal measured with in-house chromium radiation Authors: Liang, Y.H. / Zhou, Y.F. / Li, L.F. / Su, X.D. / Yang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bgk.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bgk.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/3bgk ftp://data.pdbj.org/pub/pdb/validation_reports/bg/3bgk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34095.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU.573 / Plasmid: pET-28a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8DVC0 |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-K / |
#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: 1.92 Å3/Da / Density % sol: 36 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 0.49M sodium phosphate monobasic monohydrate, 0.91M Potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 2.2909 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 20, 2007 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: multilayers optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 2.2909 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 10 % / Av σ(I) over netI: 32.1 / Number: 93650 / Rmerge(I) obs: 0.051 / Χ2: 1.1 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 9331 / % possible obs: 80.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.5→25 Å / Num. obs: 8542 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.86 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 29.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 20.4 / Num. unique all: 629 / Rsym value: 0.078 / % possible all: 69.7 |
-Phasing
Phasing | Method: MAD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 9331 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.869 / SU B: 9.284 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.225 Å2
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Refine analyze | Luzzati coordinate error obs: 0.317 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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