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Yorodumi- PDB-3boy: Crystal structure of the HutP antitermination complex bound to th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3boy | |||||||||
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Title | Crystal structure of the HutP antitermination complex bound to the HUT mRNA | |||||||||
Components |
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Keywords | 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 | Function and homology information histidine metabolic process / mRNA binding / positive regulation of gene expression Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Kumarevel, T.S. / Balasundaresan, D. / Jeyakanthan, J. / Shinkai, A. / Yokoyama, S. / Kumar, P.K.R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: To be Published 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: Journal: Structure / Year: 2004 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: Journal: Nature / Year: 2005 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: Journal: Nucleic Acids Res. / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3boy.cif.gz | 121.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3boy.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 3boy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/3boy ftp://data.pdbj.org/pub/pdb/validation_reports/bo/3boy | HTTPS FTP |
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-Related structure data
Related structure data | 1wmqS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-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.) Bacillus subtilis (bacteria) / Gene: hutP / Plasmid: Pet5A, PETHP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P10943 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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