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Yorodumi- PDB-5h3r: Crystal Structure of mutant MarR C80S from E.coli complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h3r | ||||||
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Title | Crystal Structure of mutant MarR C80S from E.coli complexed with operator DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / MarR family protein / HTH motif / protein-DNA complex / Transcription Factor / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information response to stress / cellular response to antibiotic / response to heat / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | Zhu, R. / Lou, H. / Hao, Z. | ||||||
Citation | Journal: J. Biol. Inorg. Chem. / Year: 2017 Title: Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator. Authors: Zhu, R. / Hao, Z. / Lou, H. / Song, Y. / Zhao, J. / Chen, Y. / Zhu, J. / Chen, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h3r.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h3r.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 5h3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h3r_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 5h3r_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 5h3r_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 5h3r_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/5h3r ftp://data.pdbj.org/pub/pdb/validation_reports/h3/5h3r | HTTPS FTP |
-Related structure data
Related structure data | 3q5fS 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
#1: DNA chain | Mass: 6413.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: DNA chain | Mass: 6471.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Protein | Mass: 16353.234 Da / Num. of mol.: 2 / Mutation: C80S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: marR, cfxB, inaR, soxQ, b1530, JW5248 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27245 #4: 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: 3.14 Å3/Da / Density % sol: 60.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG 5000 MME, sodium cacodylate, magnesium chloride, sodium chloride PH range: 5.6-6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0055 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0055 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→50 Å / Num. all: 16064 / Num. obs: 16057 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 55.4 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 24.03 |
Reflection shell | Resolution: 2.67→2.72 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q5F Resolution: 2.67→33.717 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.88 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.67→33.717 Å
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Refine LS restraints |
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LS refinement shell |
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