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Yorodumi- PDB-1wmq: Structure of the HutP antitermination complex bound to a single s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wmq | ||||||
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Title | Structure of the HutP antitermination complex bound to a single stranded region of hut mRNA | ||||||
Components |
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Keywords | TRANSCRIPTION/RNA / HutP / protein-RNA complex / Antitermination / RNA binding / Transcription regulation / TRANSCRIPTION-RNA COMPLEX | ||||||
Function / homology | Function and homology information L-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: 1.6 Å | ||||||
Authors | Kumarevel, T.S. / Mizuno, H. / Kumar, P.K.R. | ||||||
Citation | 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. #1: 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.R. #2: 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.S. / Fujimoto, Z. / Karthe, P. / Oda, M. / 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 | 1wmq.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wmq.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/1wmq ftp://data.pdbj.org/pub/pdb/validation_reports/wm/1wmq | HTTPS FTP |
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-Related structure data
Related structure data | 1wpsC 1wpvC 1veaS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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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 |
-Components
#1: RNA chain | Mass: 2160.283 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.) Bacillus subtilis (bacteria) / Plasmid: pET5a / Production host: Escherichia coli (E. coli) / Strain (production host): pETHP4 / References: UniProt: P10943 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 30.3 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: MPD, magnesium chloride, HEPES, 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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2004 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 38073 / Num. obs: 38073 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.029 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.258 / Num. unique all: 3787 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VEA Resolution: 1.6→19.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1932839.51 / 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: 71.1572 Å2 / ksol: 0.359632 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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