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- PDB-3keo: Crystal Structure of a Rex-family transcriptional regulatory prot... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3keo | ||||||
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Title | Crystal Structure of a Rex-family transcriptional regulatory protein from Streptococcus agalactiae complexed with NAD+ | ||||||
![]() | Redox-sensing transcriptional repressor rex | ||||||
![]() | TRANSCRIPTION / DNA binding protein / winged helix / Rossmann fold / NAD+ / Repressor / Transcription regulation / Redox sensing | ||||||
Function / homology | ![]() response to redox state / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thiyagarajan, S. / Logan, D. / von Wachenfeldt, C. | ||||||
![]() | ![]() Title: NAD+ pool depletion as a signal for the Rex regulon involved in Streptococcus agalactiae virulence. Authors: Franza, T. / Rogstam, A. / Thiyagarajan, S. / Sullivan, M.J. / Derre-Bobillot, A. / Bauer, M.C. / Goh, K.G.K. / Da Cunha, V. / Glaser, P. / Logan, D.T. / Ulett, G.C. / von Wachenfeldt, C. / Gaudu, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.1 KB | Display | ![]() |
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PDB format | ![]() | 161 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3keqC ![]() 3ketC ![]() 2dt5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23850.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NEM316 / Gene: gbs1167, rex / Plasmid: pET101 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 6000, 175mM magnesium chloride, 100mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2009 / Details: mirrors |
Radiation | Monochromator: Bent Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0379 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→27.1 Å / Num. all: 63360 / Num. obs: 62064 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.42 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.26 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DT5 Resolution: 1.5→27.07 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.624 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→27.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.499→1.538 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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