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Yorodumi- PDB-8c7u: Transcriptional pleiotropic repressor CodY from Enterococcus faec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c7u | ||||||
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Title | Transcriptional pleiotropic repressor CodY from Enterococcus faecalis in complex with Leu and a 30-bp DNA fragment encompassing two overlapping binding sites | ||||||
Components |
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Keywords | TRANSCRIPTION / LEUCINE BINDING / PLEIOTROPIC TRANSCRIPTION / REGULATOR / DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / GTP binding / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Hainzl, T. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Structural insights into CodY activation and DNA recognition. Authors: Hainzl, T. / Bonde, M. / Almqvist, F. / Johansson, J. / Sauer-Eriksson, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c7u.cif.gz | 241.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c7u.ent.gz | 190.7 KB | Display | PDB format |
PDBx/mmJSON format | 8c7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/8c7u ftp://data.pdbj.org/pub/pdb/validation_reports/c7/8c7u | HTTPS FTP |
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-Related structure data
Related structure data | 8c7oC 8c7sC 8c7tC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29083.346 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria) Gene: codY, CGZ46_07460, CUM81_01520, DAI13_08275, EY666_04655, GTI81_07970, H9Q64_02750, JFI91_04250 Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B4XP18 #2: DNA chain | | Mass: 9178.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) #3: DNA chain | | Mass: 9259.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) #4: Chemical | #5: Chemical | ChemComp-MN / | Has ligand of interest | Y | |
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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: 2.67 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Protein,200 microM in 20 mM TrisCl pH 8, 150 mM NaCl,4 mM Leu, 60 microM DNA Well, 0.01 M CoCl2, 0.01 M MnCl2, 0.1 M NaAc pH 4.6,1 M 1,6-Hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9116 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→48.79 Å / Num. obs: 25663 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 112 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.073 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.15→3.26 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2516 / CC1/2: 0.441 / Rpim(I) all: 1.01 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→48.79 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.56 / 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: 3.15→48.79 Å
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Refine LS restraints |
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LS refinement shell |
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