+Open data
-Basic information
Entry | Database: PDB / ID: 5ywj | |||||||||||||||
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Title | Global regulatory element SarX | |||||||||||||||
Components | HTH-type transcriptional regulator SarX | |||||||||||||||
Keywords | TRANSCRIPTION / Global regulatory element / DNA-binding / transcriptional contral | |||||||||||||||
Function / homology | Transcriptional regulator SarA/Rot / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / regulation of DNA-templated transcription / DNA binding / cytoplasm / HTH-type transcriptional regulator SarX Function and homology information | |||||||||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å | |||||||||||||||
Authors | Wang, Q. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: To Be Published Title: Crystal structure of SarX from Staphylococcus aureus Authors: Wang, Q. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ywj.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ywj.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ywj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/5ywj ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5ywj | HTTPS FTP |
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-Related structure data
Related structure data | 6k8eC 5hs5S 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: 15030.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria) Strain: NCTC 8325 / Gene: sarX, SAOUHSC_00674 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q2G0D1 |
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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: 2.14 Å3/Da / Density % sol: 42.56 % |
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Crystal grow | Temperature: 289.16 K / Method: vapor diffusion, sitting drop / Details: Bicine pH9.0, 1,4-Dioxane, PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å |
Detector | Type: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Jun 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97774 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→57.74 Å / Num. obs: 8345 / % possible obs: 98.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 8.19 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.221 / Num. unique obs: 557 / Rsym value: 0.221 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HS5 Resolution: 2.102→23.612 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.4 / Phase error: 32.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.102→23.612 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: 14.0315 Å / Origin y: 10.4895 Å / Origin z: 16.1537 Å
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Refinement TLS group | Selection details: all |