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Yorodumi- PDB-1q08: Crystal structure of the Zn(II) form of E. coli ZntR, a zinc-sens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q08 | ||||||
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Title | Crystal structure of the Zn(II) form of E. coli ZntR, a zinc-sensing transcriptional regulator, at 1.9 A resolution (space group P212121) | ||||||
Components | Zn(II)-responsive regulator of zntA | ||||||
Keywords | TRANSCRIPTION / MerR family transcriptional regulator / Zn(II)-responsive regulator of zntA | ||||||
Function / homology | Function and homology information DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / zinc ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å | ||||||
Authors | Changela, A. / Chen, K. / Xue, Y. / Holschen, J. / Outten, C.E. / O'Halloran, T.V. / Mondragon, A. | ||||||
Citation | Journal: Science / Year: 2003 Title: Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR Authors: Changela, A. / Chen, K. / Xue, Y. / Holschen, J. / Outten, C.E. / O'Halloran, T.V. / Mondragon, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q08.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q08.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 1q08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/1q08 ftp://data.pdbj.org/pub/pdb/validation_reports/q0/1q08 | HTTPS FTP |
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-Related 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: 11111.611 Da / Num. of mol.: 2 / Fragment: ZntR dimerization and metal-binding domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ZNTR / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ACS5 #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / | #5: 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: 2.62 Å3/Da / Density % sol: 53.09 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium phosphate dibasic, MES, sodium chloride, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29 Å / Num. all: 50994 / Num. obs: 18897 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.066 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1365 / Rsym value: 0.285 / % possible all: 99 |
Reflection | *PLUS Num. measured all: 50994 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.9→28.83 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1125381.48 / Data cutoff high rms absF: 1125381.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.3864 Å2 / ksol: 0.404718 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→28.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 29 Å / Num. reflection obs: 17949 / % reflection Rfree: 7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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