[English] 日本語
Yorodumi- PDB-3zzs: Engineered 12-subunit Bacillus stearothermophilus trp RNA-binding... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zzs | ||||||
---|---|---|---|---|---|---|---|
Title | Engineered 12-subunit Bacillus stearothermophilus trp RNA-binding attenuation protein (TRAP) | ||||||
Components | TRANSCRIPTION ATTENUATION PROTEIN MTRB | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION REGULATION / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | GEOBACILLUS STEAROTHERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zzs.cif.gz | 288.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zzs.ent.gz | 239.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/3zzs ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zzs | HTTPS FTP |
---|
-Related structure data
Related structure data | 3zzlC 3zzqC 1qawS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 7216.196 Da / Num. of mol.: 9 / Fragment: RESIDUES 5-69 Source method: isolated from a genetically manipulated source Details: THE LAST FIVE RESIDUES ARE REMOVED IN B. STEAROTHERMOPHILUS TRAP E71STOP Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X6J6 #2: Chemical | ChemComp-TRP / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.5 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→25 Å / Num. obs: 124338 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.49→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QAW Resolution: 1.49→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.888 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.058 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|