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- PDB-1wpu: Crystal Structure of the HutP antitermination complex bound to a ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wpu | ||||||
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Title | Crystal Structure of the HutP antitermination complex bound to a single stranded region of hut mRNA | ||||||
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![]() | TRANSCRIPTION/RNA / HutP / RNA binding / HutP-RNA complex / Antitermination / Transcription regulation / TRANSCRIPTION-RNA COMPLEX | ||||||
Function / homology | ![]() L-histidine metabolic process / mRNA binding / positive regulation of gene expression Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumarevel, T.S. / Mizuno, H. / Kumar, P.K.R. | ||||||
![]() | ![]() Title: Structural basis for the HutP antitermination Complex:Role of divalent metal ions in allosteric activation Authors: Kumarevel, T.S. / Mizuno, H. / 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.S. / 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.S. / Gopinath, S.C. / Nishikawa, S. / Mizuno, H. / Kumar, P.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 64.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.9 KB | Display | ![]() |
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Full document | ![]() | 491.3 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1veaS S: Starting model for refinement |
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Similar structure data |
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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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Details | The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y, x-y, z and -x+y, -x, z |
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Components
#1: RNA chain | Mass: 2199.323 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 16101.357 Da / Num. of mol.: 2 / Mutation: V51I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 26.9 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: MPD, HEPES, MgCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2004 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. all: 47155 / Num. obs: 47155 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.042 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.314 / Num. unique all: 4826 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1VEA Resolution: 1.48→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1551356.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 76.8352 Å2 / ksol: 0.359595 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.48→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.57 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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