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Yorodumi- PDB-3zzq: Engineered 12-subunit Bacillus subtilis trp RNA-binding attenuati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zzq | ||||||
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Title | Engineered 12-subunit Bacillus subtilis trp RNA-binding attenuation protein (TRAP) | ||||||
Components | TRANSCRIPTION ATTENUATION PROTEIN MTRB | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information positive regulation of termination of DNA-templated transcription / negative regulation of translational initiation / DNA-templated transcription termination / RNA binding Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Chen, C. / Smits, C. / Dodson, G.G. / Shevtsov, M.B. / Merlino, N. / Gollnick, P. / Antson, A.A. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: How to Change the Oligomeric State of a Circular Protein Assembly: Switch from 11-Subunit to 12-Subunit Trap Suggests a General Mechanism Authors: Chen, C. / Smits, C. / Dodson, G.G. / Shevtsov, M.B. / Merlino, N. / Gollnick, P. / Antson, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zzq.cif.gz | 184 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zzq.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zzq_validation.pdf.gz | 484.2 KB | Display | wwPDB validaton report |
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Full document | 3zzq_full_validation.pdf.gz | 492.6 KB | Display | |
Data in XML | 3zzq_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 3zzq_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/3zzq ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zzq | HTTPS FTP |
-Related structure data
Related structure data | 3zzlC 3zzsC 1qawS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 7141.097 Da / Num. of mol.: 6 / Fragment: RESIDUES 7-71 Source method: isolated from a genetically manipulated source Details: THE LAST FOUR RESIDUES ARE REMOVED IN B.SUBTILIS TRAP. K71STOP CODON Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P19466 #2: Chemical | ChemComp-TRP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.2 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→25 Å / Num. obs: 51357 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 25.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 42.9 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 6.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QAW Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.576 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.089 / 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: 22.549 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→25 Å
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Refine LS restraints |
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