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Yorodumi- PDB-5dmb: Crystal structure of a translational regulator bound to a flagell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dmb | ||||||
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Title | Crystal structure of a translational regulator bound to a flagellar assembly factor | ||||||
Components |
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Keywords | TRANSLATION / flagellum / assembly factor | ||||||
Function / homology | Function and homology information regulation of bacterial-type flagellum assembly / regulation of carbohydrate metabolic process / bacterial-type flagellum organization / bacterial-type flagellum assembly / mRNA catabolic process / negative regulation of translational initiation / mRNA 5'-UTR binding / regulation of translation / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus thermodenitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å | ||||||
Authors | Altegoer, F. / Bange, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural basis for the CsrA-dependent modulation of translation initiation by an ancient regulatory protein. Authors: Altegoer, F. / Rensing, S.A. / Bange, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dmb.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dmb.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 5dmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dmb_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 5dmb_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 5dmb_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 5dmb_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/5dmb ftp://data.pdbj.org/pub/pdb/validation_reports/dm/5dmb | HTTPS FTP |
-Related structure data
Related structure data | 5dmdC 5jakC 2aj7S 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: 17389.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria) Gene: fliW, GTNG_3059 / Plasmid: pET24d(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4ISV0 |
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#2: Protein | Mass: 9149.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria) Gene: csrA, GTNG_3058 / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4ISU9 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium fluoride, 20 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42.48 Å / Num. obs: 11552 / % possible obs: 99.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 1.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Rmerge(I) obs: 0.518 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AJ7 Resolution: 2.301→42.477 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.18 / 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 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.301→42.477 Å
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Refine LS restraints |
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LS refinement shell |
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