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Yorodumi- PDB-8c7s: Transcriptional pleiotropic repressor CodY from Staphylococcus au... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c7s | ||||||
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Title | Transcriptional pleiotropic repressor CodY from Staphylococcus aureus in complex with Ile, GTP, and a 30-bp DNA fragment encompassing two overlapping binding sites | ||||||
Components |
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Keywords | TRANSCRIPTION / GTP SENSING / PLEIOTROPIC TRANSCRIPTION REGULATOR / GTP / 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 | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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 | 8c7s.cif.gz | 151.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c7s.ent.gz | 113 KB | Display | PDB format |
PDBx/mmJSON format | 8c7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/8c7s ftp://data.pdbj.org/pub/pdb/validation_reports/c7/8c7s | HTTPS FTP |
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-Related structure data
Related structure data | 8c7oC 8c7tC 8c7uC 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
-DNA chain , 2 types, 2 molecules MN
#1: DNA chain | Mass: 9178.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) |
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#2: DNA chain | Mass: 9259.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) |
-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 28666.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria) Gene: codY / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B0CMV4 |
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-Non-polymers , 4 types, 16 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
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: 3 Å3/Da / Density % sol: 59.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Protein, 140 microM, 20 mM TrisCl pH 8, 150 mM NaCl, 20 mM Ile, 2 mM GTP, 35 microM dsDNA, 3% DMSO Well, 150 mM ammoniumsulphate,100 mM MES pH 5.4, 23-25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→44.7 Å / Num. obs: 16453 / % possible obs: 99.9 % / Redundancy: 23.2 % / Biso Wilson estimate: 69.2 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.109 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 24.4 % / Rmerge(I) obs: 2.567 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1599 / CC1/2: 0.824 / Rpim(I) all: 0.733 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→44.68 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→44.68 Å
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Refine LS restraints |
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LS refinement shell |
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