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Yorodumi- PDB-3ket: Crystal structure of a Rex-family transcriptional regulatory prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ket | ||||||
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Title | Crystal structure of a Rex-family transcriptional regulatory protein from Streptococcus agalactiae bound to a palindromic operator | ||||||
Components |
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Keywords | Transcription/DNA / Protein-DNA complex / Winged helix / Rossmann fold / NAD+ / Repressor / Transcription / Transcription regulation / REDOX sensing / Transcription-DNA complex | ||||||
Function / homology | Function and homology information response to redox state / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus agalactiae serogroup III (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Thiyagarajan, S. / Logan, D. / von Wachenfeldt, C. | ||||||
Citation | Journal: Plos Pathog. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ket.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ket.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ket.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ket_validation.pdf.gz | 762 KB | Display | wwPDB validaton report |
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Full document | 3ket_full_validation.pdf.gz | 770.6 KB | Display | |
Data in XML | 3ket_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 3ket_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/3ket ftp://data.pdbj.org/pub/pdb/validation_reports/ke/3ket | HTTPS FTP |
-Related structure data
Related structure data | 3keoSC 3keqC C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23850.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serogroup III (bacteria) Strain: NEM316 / Gene: gbs1167, rex / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: Q8E565 |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3396.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 121 molecules
#4: Chemical | ChemComp-NAD / |
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#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 22 % PEG 1500, 50mM MIB, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 3, 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: 2.4→29.49 Å / Num. all: 16223 / Num. obs: 16157 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.67 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.04 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KEO and a fiber model double stranded B-DNA of length 11 base pairs Resolution: 2.4→29.49 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 13.041 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.238 / 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: 32.429 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 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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