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Yorodumi- PDB-1wrn: Metal Ion dependency of the antiterminator protein, HutP, for bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wrn | ||||||
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Title | Metal Ion dependency of the antiterminator protein, HutP, for binding to the terminator region of hut mRNA- A structural basis | ||||||
Components | Hut operon positive regulatory protein | ||||||
Keywords | RNA BINDING PROTEIN / HutP / Antitermination / L-histidine / metal ions / conformational change | ||||||
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: 2.3 Å | ||||||
Authors | Kumarevel, T. / Mizuno, H. / Kumar, P.K.R. | ||||||
Citation | 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. #1: 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. #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. / Fujimoto, Z. / Karthe, P. / Oda, M. / Mizuno, H. / Kumar, P.K.R. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wrn.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wrn.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 1wrn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/1wrn ftp://data.pdbj.org/pub/pdb/validation_reports/wr/1wrn | HTTPS FTP |
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-Related structure data
-Links
-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 thr trimer in the asymmetric unit by the operation 1-x, -y, z (2_655) |
-Components
#1: 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) / Plasmid: pET5a / Production host: Escherichia coli (E. coli) / Strain (production host): pETHP4 / References: UniProt: P10943 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / #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: 2.5 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG550, MnCl2, MPD, HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 19, 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: 2.2→50 Å / Num. all: 24576 / Num. obs: 24576 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.036 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.258 / Num. unique all: 2408 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.66 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1350003.91 / 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: 85.293 Å2 / ksol: 0.294921 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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