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- PDB-1q0a: Crystal structure of the Zn(II) form of E. coli ZntR, a zinc-sens... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q0a | ||||||
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Title | Crystal structure of the Zn(II) form of E. coli ZntR, a zinc-sensing transcriptional regulator (space group C222) | ||||||
![]() | Zn(II)-responsive regulator of zntA | ||||||
![]() | TRANSCRIPTION / MerR family transcriptional regulator / Zn(II)-responsive regulator of zntA | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Changela, A. / Chen, K. / Xue, Y. / Holschen, J. / Outten, C.E. / O'Halloran, T.V. / Mondragon, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.3 KB | Display | ![]() |
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PDB format | ![]() | 37.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.2 KB | Display | ![]() |
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Full document | ![]() | 438.2 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | For chain A, apply the following symmetry operations to generate the biologically significant dimer: -x, y, -z / For chain B, apply the following symmetry operations to generate the biologically significant dimer: 1-x, y, 2-z |
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Components
#1: Protein | Mass: 11111.611 Da / Num. of mol.: 2 / Fragment: Dimerization and metal-binding domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.15 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Na/K tartrate, Hepes, pH 7.5, 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 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: 1.98→24 Å / Num. obs: 21722 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.039 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1339 / Rsym value: 0.156 / % possible all: 83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ZntR in P212121 crystal form Resolution: 2→23.59 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1440953.75 / Data cutoff high rms absF: 1440953.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: partially refined structure
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.9013 Å2 / ksol: 0.38242 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→23.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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