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Yorodumi- PDB-4b27: Trp RNA-binding attenuation protein: modifying symmetry and stabi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b27 | ||||||
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Title | Trp RNA-binding attenuation protein: modifying symmetry and stability of a circular oligomer | ||||||
Components | TRANSCRIPTION ATTENUATION PROTEIN MTRB | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION / THERMOFLUOR / 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: 2.72 Å | ||||||
Authors | Bayfield, O.W. / Chen, C. / Patterson, A.R. / Luan, W. / Smits, C. / Gollnick, P. / Antson, A.A. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Trp RNA-Binding Attenuation Protein: Modifying Symmetry and Stability of a Circular Oligomer. Authors: Bayfield, O.W. / Chen, C. / Patterson, A.R. / Luan, W. / Smits, C. / 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 | 4b27.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b27.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 4b27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/4b27 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/4b27 | HTTPS FTP |
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-Related structure data
Related structure data | 3zzqS 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: 8370.505 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19466 #2: Chemical | ChemComp-TRP / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 72 TO ASN ENGINEERED RESIDUE IN CHAIN B, SER 72 TO ASN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | Details: 100 MM BIS-TRIS PROPANE (PH 8.5), 200 MM KSCN AND 13% PEG 3350 (V/V) |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9163 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9163 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. obs: 14253 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 86.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.8 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZZQ Resolution: 2.72→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 38.109 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.984 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 115.973 Å2
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Refinement step | Cycle: LAST / Resolution: 2.72→25 Å
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Refine LS restraints |
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