+Open data
-Basic information
Entry | Database: PDB / ID: 3mex | ||||||
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Title | Crystal structure of MexR in oxidized state | ||||||
Components | Multidrug resistance operon repressor | ||||||
Keywords | Transcription / Transcription Regulation / antibiotics resistance regulation / oxidative stress / thiol modification / DNA-binding | ||||||
Function / homology | Function and homology information negative regulation of transmembrane transport / DNA-binding transcription repressor activity / negative regulation of protein secretion / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Chen, H. / Yi, C. / Zhang, J. / Zhang, W. / Yang, C.-G. / He, C. | ||||||
Citation | Journal: Embo Rep. / Year: 2010 Title: Structural insight into the oxidation-sensing mechanism of the antibiotic resistance of regulator MexR Authors: Chen, H. / Yi, C. / Zhang, J. / Zhang, W. / Ge, Z. / Yang, C.-G. / He, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mex.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mex.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/3mex ftp://data.pdbj.org/pub/pdb/validation_reports/me/3mex | HTTPS FTP |
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-Related structure data
Related structure data | 1lnwS 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: Protein | Mass: 16403.852 Da / Num. of mol.: 2 / Fragment: residue 1-142 / Mutation: C138S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: MEXR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52003 #2: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.8M sodium acetate trihydrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 31715 / Num. obs: 17076 / % possible obs: 99.7 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 7.1 % / Rmerge(I) obs: 0.078 / Rsym value: 0.055 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 6 / Num. unique all: 1675 / Rsym value: 0.379 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LNW Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.036 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 6 / σ(I): 6 / ESU R: 0.28 / ESU R Free: 0.215 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.103 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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