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Yorodumi- PDB-5ft1: Crystal structure of gp37(Dip) from bacteriophage phiKZ bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ft1 | ||||||
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Title | Crystal structure of gp37(Dip) from bacteriophage phiKZ bound to RNase E of Pseudomonas aeruginosa | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / DIP / PHIKZ / BACTERIOPHAGE / RNASE E / RIBONUCLEASE INHIBITOR / RNA DEGRADOSOME / PSEUDOMONAS AERUGINOSA | ||||||
Function / homology | Function and homology information ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding ...ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding / magnesium ion binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | PSEUDOMONAS PHAGE PHIKZ (virus) PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Van den Bossche, A. / Hardwick, S.W. / Ceyssens, P.J. / Hendrix, H. / Voet, M. / Dendooven, T. / Bandyra, K.J. / De Maeyer, M. / Aertsen, A. / Noben, J.P. ...Van den Bossche, A. / Hardwick, S.W. / Ceyssens, P.J. / Hendrix, H. / Voet, M. / Dendooven, T. / Bandyra, K.J. / De Maeyer, M. / Aertsen, A. / Noben, J.P. / Luisi, B.F. / Lavigne, R. | ||||||
Citation | Journal: Elife / Year: 2016 Title: Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome. Authors: Van den Bossche, A. / Hardwick, S.W. / Ceyssens, P.J. / Hendrix, H. / Voet, M. / Dendooven, T. / Bandyra, K.J. / De Maeyer, M. / Aertsen, A. / Noben, J.P. / Luisi, B.F. / Lavigne, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ft1.cif.gz | 298.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ft1.ent.gz | 239.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ft1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ft1_validation.pdf.gz | 519.4 KB | Display | wwPDB validaton report |
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Full document | 5ft1_full_validation.pdf.gz | 564.2 KB | Display | |
Data in XML | 5ft1_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 5ft1_validation.cif.gz | 74.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/5ft1 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/5ft1 | HTTPS FTP |
-Related structure data
Related structure data | 5ft0SC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 31991.303 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS PHAGE PHIKZ (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q8SDC5 #2: Protein/peptide | Mass: 2704.057 Da / Num. of mol.: 6 / Fragment: RESIDUES 756-775 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: Q9HZM8, ribonuclease E #3: 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: 2.37 Å3/Da / Density % sol: 48.16 % Description: DATA PROCESSED IN LOW SYMMETRY P1 SPACE GROUP AS REFINEMENT STATISTICS AND ELECTRON DENSITY FOR BOUND PEPTIDE WERE MARGINALLY BETTER THAN IN RECOMMENDED H32 SPACE GROUP |
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Crystal grow | Details: 100 MM KH2PO4, 100 MM NAH2PO4, 100 MM MES PH 6.0, 300 MM NACL, 0.2 M SODIUM THIOCYANATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection twin | Operator: -L,-K,-H / Fraction: 0.5 |
Reflection | Resolution: 2.75→72.2 Å / Num. obs: 39553 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.75→2.84 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.7 / % possible all: 93.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FT0 Resolution: 2.75→72.188 Å / σ(F): 1.98 / Phase error: 32.82 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→72.188 Å
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Refine LS restraints |
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LS refinement shell |
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