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Yorodumi- PDB-3zqf: Structure of Tetracycline repressor in complex with antiinducer p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zqf | ||||||
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Title | Structure of Tetracycline repressor in complex with antiinducer peptide-TAP1 | ||||||
Components |
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Keywords | TRANSCRIPTION / TETRACYCLINE REPRESSOR / TETR / INDUCERS / PEPTIDIC EFFECTORS / ALLOSTERY | ||||||
Function / homology | Function and homology information response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Sevvana, M. / Goeke, D. / Stoeckle, C. / Kaspar, D. / Grubmueller, S. / Goetz, C. / Wimmer, C. / Berens, C. / Klotzsche, M. / Muller, Y.A. / Hillen, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: An Exclusive Alpha/Beta Code Directs Allostery in Tetr-Peptide Complexes. Authors: Sevvana, M. / Goetz, C. / Goeke, D. / Wimmer, C. / Berens, C. / Hillen, W. / Muller, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zqf.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zqf.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zqf ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zqf | HTTPS FTP |
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-Related structure data
Related structure data | 3zqgC 3zqhC 3zqiC 2ns8S C: citing same article (ref.) 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: 23531.662 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-187,188-208 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUES 1-187 ARE FROM VARIANT B, RESIDUES 188-208 ARE FROM VARIANT D Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04483, UniProt: P0ACT4 |
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#2: Protein/peptide | Mass: 1659.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 68 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 88 TO ASN ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 71.6 % / Description: NONE |
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Crystal grow | pH: 6 / Details: RESERVOIR: 3 M NACL, 0.1 M BIS-TRIS, PH 6. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH MX-225 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→20 Å / Num. obs: 13467 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.21 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.78 |
Reflection shell | Resolution: 2.56→2.71 Å / Redundancy: 4.16 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.53 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NS8 Resolution: 2.56→32.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 23.185 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.224 / 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: 83.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→32.18 Å
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Refine LS restraints |
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