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- PDB-3boy: Crystal structure of the HutP antitermination complex bound to th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3boy | |||||||||
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Title | Crystal structure of the HutP antitermination complex bound to the HUT mRNA | |||||||||
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![]() | TRANSCRIPTION/RNA / HutP / RNA-binding / HutP-RNA Complex / Anti-termination / Transcription regulation / Activator / Histidine metabolism / TRANSCRIPTION-RNA COMPLEX / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | ![]() L-histidine metabolic process / mRNA binding / positive regulation of gene expression Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kumarevel, T.S. / Balasundaresan, D. / Jeyakanthan, J. / Shinkai, A. / Yokoyama, S. / Kumar, P.K.R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
![]() | ![]() Title: Crystal Structure of HutP complexed with the 55-mer RNA Authors: Kumarevel, T. / Balasundaresan, D. / Jeyakanthan, J. / Shinkai, A. / Yokoyama, S. / Kumar, P.K.R. #1: ![]() Title: Crystal Structure of Activated HutP: An RNA Binding Protein that Regulates Transcription of the hut Operon in Bacillus subtilis Authors: Kumarevel, T. / Fujimoto, Z. / Karthe, P. / Oda, M. / Mizuno, H. / Kumar, P.K.R. #2: Journal: NUCLEIC ACIDS RES. / Year: 2004 Title: Identification of important chemical groups of the hut mRNA for HutP interactions that regulate the hut operon in Bacillus subtilis Authors: Kumarevel, T. / Gopinath, S.C.B. / Nishikawa, S. / Mizuno, H. / Kumar, P.K.R. #3: ![]() Title: Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand Authors: Kumarevel, T. / Mizuno, H. / Kumar, P.K.R. #4: ![]() Title: Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis Authors: Kumarevel, T. / Mizuno, H. / Kumar, P.K.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.8 KB | Display | ![]() |
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PDB format | ![]() | 91.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.2 KB | Display | ![]() |
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Full document | ![]() | 500.4 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wmqS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 6876.931 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||||
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#2: Protein | Mass: 16101.357 Da / Num. of mol.: 3 / Mutation: V51I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.96 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 40% MPD, 0.1M HEPES, 0.1M MGCL2, pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2006 |
Radiation | Monochromator: SI II Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 48341 / Num. obs: 48341 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.045 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.362 / Num. unique all: 4735 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WMQ Resolution: 1.7→38.24 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.627 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 28.961 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→38.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.703→1.747 Å / Total num. of bins used: 20
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