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Yorodumi- PDB-3jth: Crystal structure of a transcriptional regulator HlyU from Vibrio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jth | ||||||
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Title | Crystal structure of a transcriptional regulator HlyU from Vibrio vulnificus CMCP6 | ||||||
Components | Transcription activator HlyU | ||||||
Keywords | TRANSCRIPTION / transcription factor / HlyU / rtxA / DNA-binding / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Nishi, K. / Lee, H.J. / Park, S.Y. / Kim, J.S. | ||||||
Citation | Journal: Febs Lett. / Year: 2010 Title: Crystal structure of the transcriptional activator HlyU from Vibrio vulnificus CMCP6. Authors: Nishi, K. / Lee, H.J. / Park, S.Y. / Bae, S.J. / Lee, S.E. / Adams, P.D. / Rhee, J.H. / Kim, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jth.cif.gz | 46 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jth.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 3jth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jth_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 3jth_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 3jth_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 3jth_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/3jth ftp://data.pdbj.org/pub/pdb/validation_reports/jt/3jth | HTTPS FTP |
-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: 11451.799 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: VV1_0512 / Plasmid: pProExHTc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8DES3, UniProt: A0A3Q0L222*PLUS #2: 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: 1.92 Å3/Da / Density % sol: 36.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 9~11% polyethylene glycol 20000, 0.1M Sodium Acetate, 0.1M (N-Morpholino) propanesulfonic acid, pH6.5, 10mM b-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 28, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 13719 / Num. obs: 12896 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.078 / Rsym value: 0.065 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.94 / Num. unique all: 1343 / Rsym value: 0.225 / % possible all: 76.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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