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Yorodumi- PDB-4u0v: Crystal structure of YvoA from Bacillus subtilis in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u0v | |||||||||
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Title | Crystal structure of YvoA from Bacillus subtilis in complex with glucosamine-6-phosphate | |||||||||
Components | HTH-type transcriptional repressor YvoA | |||||||||
Keywords | TRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Chorismate lyase fold / N-acetylglucosamine utilization | |||||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å | |||||||||
Authors | Fillenberg, S.B. / Muller, Y.A. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR. Authors: Fillenberg, S.B. / Grau, F.C. / Seidel, G. / Muller, Y.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u0v.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u0v.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 4u0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/4u0v ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u0v | HTTPS FTP |
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-Related structure data
Related structure data | 4u0wC 4u0yC 4wwcC 2wv0S 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: 27823.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: yvoA, BSU35030 / Production host: Escherichia coli (E. coli) / References: UniProt: O34817 #2: Sugar | #3: Chemical | ChemComp-EDO / #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: 3 Å3/Da / Density % sol: 59.05 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Na-HEPES salt, 200 mM ammonium chloride, 25 % (v/v) glycerol ethoxylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 5, 2012 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→32.65 Å / Num. obs: 42017 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.39 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.43 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2wv0 Resolution: 2.051→32.647 Å / Occupancy max: 1 / Occupancy min: 0.27 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.98 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.71 Å2 / Biso mean: 38.5034 Å2 / Biso min: 19.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.051→32.647 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: 15
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