+Open data
-Basic information
Entry | Database: PDB / ID: 1qpi | ||||||
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Title | CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / REPRESSOR-OPERATOR COMPLEX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Orth, P. / Schnappinger, D. / Hillen, W. / Saenger, W. / Hinrichs, W. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Authors: Orth, P. / Schnappinger, D. / Hillen, W. / Saenger, W. / Hinrichs, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qpi.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qpi.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/1qpi ftp://data.pdbj.org/pub/pdb/validation_reports/qp/1qpi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4577.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA SEQUENCE TAKEN FROM TET OPERATOR CLASS D |
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#2: DNA chain | Mass: 4599.008 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 22831.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): K12 DELTA H1 DELTA TRP / References: UniProt: P0ACT4 |
#4: Chemical | ChemComp-IMD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS 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: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 28, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→34.5 Å / Num. obs: 12437 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.45→2.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.287 / % possible all: 93.3 |
Reflection | *PLUS Lowest resolution: 24.5 Å / Num. obs: 11520 / Num. measured all: 42624 / Biso Wilson estimate: 57.9 Å2 |
Reflection shell | *PLUS % possible obs: 94.4 % / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Resolution: 2.5→34.5 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: USED WEIGHTED FULL MATRIX LEAST SQUARE PROCEDURE. THE DNA BASE PAIRS 1, 8 AND 15 ARE NOT PALINDROMIC. IN REFINEMENT THE CENTRAL BASE M 8 WAS MODELED USING ADENINE AND THYMINE WITH 50 % ...Details: USED WEIGHTED FULL MATRIX LEAST SQUARE PROCEDURE. THE DNA BASE PAIRS 1, 8 AND 15 ARE NOT PALINDROMIC. IN REFINEMENT THE CENTRAL BASE M 8 WAS MODELED USING ADENINE AND THYMINE WITH 50 % OCCUPANCY EACH, RESPECTIVELY. BASE M 1 WAS EITHER CYTOSINE OR THYMINE AND BASE M 15 WAS EITHER GUANINE OR ADENINE. DUE TO CLOSE CRYSTAL PACKING CONTACTS THESE TERMINAL BASES WERE FOUND DISORDERED AND WERE MODELED AS CYTOSINE (BASE M 1) AND ADENINE (BASE M 15), RESPECTIVELY.
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Refinement step | Cycle: LAST / Resolution: 2.5→34.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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