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Yorodumi- PDB-3l7w: The Crystal Structure of smu.1704 from Streptococcus mutans UA159 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l7w | ||||||
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Title | The Crystal Structure of smu.1704 from Streptococcus mutans UA159 | ||||||
Components | Putative uncharacterized protein SMU.1704 | ||||||
Keywords | TRANSCRIPTION / PadR / transcriptional factor | ||||||
Function / homology | Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / PadR domain-containing protein Function and homology information | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Su, X.-D. / Liu, X. / Fu, T.M. | ||||||
Citation | Journal: TO BE PUBLISHED Title: The Crystal Structure of smu.1704 from Streptococcus mutans UA159 Authors: Su, X.-D. / Liu, X. / Fu, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l7w.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l7w.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 3l7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/3l7w ftp://data.pdbj.org/pub/pdb/validation_reports/l7/3l7w | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12804.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU.1704 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DSR7 |
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#2: 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: 3.21 Å3/Da / Density % sol: 61.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH7.5, 3.0M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 9236 / Num. obs: 9136 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 37.87 Å2 |
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 93.8 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 2.2→18.851 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.789 / SU ML: 0.33 / σ(F): 1.99 / Phase error: 25.76 / 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 / Bsol: 52.718 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.06 Å2 / Biso mean: 41.869 Å2 / Biso min: 19.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→18.851 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.2004 Å / Origin y: -23.8046 Å / Origin z: -3.3915 Å
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Refinement TLS group |
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