+Open data
-Basic information
Entry | Database: PDB / ID: 3tlq | ||||||
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Title | Crystal structure of EAL-like domain protein YdiV | ||||||
Components | Regulatory protein YdiV | ||||||
Keywords | TRANSCRIPTION / Anti-Flhd4c2 factor / Repress motility | ||||||
Function / homology | negative regulation of bacterial-type flagellum-dependent cell motility / EAL domain / EAL domain / EAL domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / PHOSPHATE ION / Putative anti-FlhC(2)FlhD(4) factor YdiV Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Li, B. / Li, N. / Wang, F. / Guo, L. / Liu, C. / Zhu, D. / Xu, S. / Gu, L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility Authors: Li, B. / Li, N. / Wang, F. / Guo, L. / Huang, Y. / Liu, X. / Wei, T. / Zhu, D. / Liu, C. / Pan, H. / Xu, S. / Wang, H.W. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tlq.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tlq.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 3tlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tlq_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 3tlq_full_validation.pdf.gz | 469.3 KB | Display | |
Data in XML | 3tlq_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 3tlq_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/3tlq ftp://data.pdbj.org/pub/pdb/validation_reports/tl/3tlq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27481.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Gene: b1707, JW1697, ydiV / Plasmid: pGL01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76204 #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: 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: 2.49 Å3/Da / Density % sol: 50.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 2.0M Sodium/Potassium phosphate PH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2010 | |||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.91→50 Å / Num. all: 41951 / Num. obs: 41951 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.14 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 17.53 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→39.635 Å / SU ML: 0.19 / σ(F): 0 / σ(I): 0 / Phase error: 19.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.925 Å2 / ksol: 0.406 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→39.635 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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