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Yorodumi- PDB-3gdw: Crystal structure of sigma-54 interaction domain protein from Ent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gdw | ||||||
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Title | Crystal structure of sigma-54 interaction domain protein from Enterococcus faecalis | ||||||
Components | Sigma-54 interaction domain protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis / sigma-54 interaction domain protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Nucleotide-binding | ||||||
Function / homology | Function and homology information phosphoenolpyruvate-dependent sugar phosphotransferase system / transcription factor binding / kinase activity / membrane => GO:0016020 / regulation of DNA-templated transcription / ATP binding Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Chang, C. / Sather, A. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of sigma-54 interaction domain protein from Enterococcus faecalis Authors: Chang, C. / Sather, A. / Buck, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gdw.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gdw.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/3gdw ftp://data.pdbj.org/pub/pdb/validation_reports/gd/3gdw | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15903.516 Da / Num. of mol.: 2 / Fragment: UNP residues 544-679 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_1010 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q836U6 #2: Chemical | ChemComp-EDO / | #3: 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: 2.29 Å3/Da / Density % sol: 46.24 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Sodium malonate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM Q315r / Detector: CCD / Date: Jan 31, 2009 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 20362 / Num. obs: 20315 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 65.7 |
Reflection shell | Resolution: 2→2.02 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 6.35 / Num. unique all: 483 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.777 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.495 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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