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- PDB-3c8g: Crystal structure of a possible transciptional regulator YggD fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c8g | |||||||||
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Title | Crystal structure of a possible transciptional regulator YggD from Shigella flexneri 2a str. 2457T | |||||||||
![]() | (Putative transcriptional regulator) x 3 | |||||||||
![]() | TRANSCRIPTION REGULATOR / APC27974 / YggD / Mannitol operon repressor / Shigella flexneri 2a str. 2457T / methylation / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tan, K. / Borovilos, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
![]() | ![]() Title: The mannitol operon repressor MtlR belongs to a new class of transcription regulators in bacteria. Authors: Tan, K. / Clancy, S. / Borovilos, M. / Zhou, M. / Horer, S. / Moy, S. / Volkart, L.L. / Sassoon, J. / Baumann, U. / Joachimiak, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.4 KB | Display | ![]() |
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PDB format | ![]() | 117.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3brjC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19893.701 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Shigella flexneri / Strain: 2457T / Serotype 2a / Gene: yggD, S3120, SF2919 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Protein | | Mass: 19893.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Shigella flexneri / Strain: 2457T / Serotype 2a / Gene: yggD, S3120, SF2919 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: ![]() ![]() #3: Protein | | Mass: 19839.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Shigella flexneri / Strain: 2457T / Serotype 2a / Gene: yggD, S3120, SF2919 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: ![]() ![]() #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% (w/v) PEG MME 2000, 0.1M Sodium acetate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Mar 29, 2006 / Details: Mirrors |
Radiation | Monochromator: Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97883 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→32 Å / Num. all: 26162 / Num. obs: 26162 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 71.63 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 30.78 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.88 / Num. unique all: 2140 / % possible all: 78.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.751 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→31.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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