+Open data
-Basic information
Entry | Database: PDB / ID: 6m7y | |||||||||
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Title | Dehydratase, NisB, bound to a non-eliminable substrate analog | |||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / RiPP / nisin / tRNA-dependent / dehydratase | |||||||||
Function / homology | Function and homology information killing of cells of another organism / defense response to bacterium / signaling receptor binding / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) Lactococcus lactis (lactic acid bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 Å | |||||||||
Authors | Cogan, D.P. / Nair, S.K. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Characterization of glutamyl-tRNA-dependent dehydratases using nonreactive substrate mimics. Authors: Bothwell, I.R. / Cogan, D.P. / Kim, T. / Reinhardt, C.J. / van der Donk, W.A. / Nair, S.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m7y.cif.gz | 418.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m7y.ent.gz | 336.6 KB | Display | PDB format |
PDBx/mmJSON format | 6m7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/6m7y ftp://data.pdbj.org/pub/pdb/validation_reports/m7/6m7y | HTTPS FTP |
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-Related structure data
Related structure data | 6ec7C 6ec8C 4wd9S 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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Unit cell |
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-Components
#1: Protein | Mass: 118647.109 Da / Num. of mol.: 2 / Mutation: V169C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Gene: nisB / Plasmid: pET28b-NisB-V169C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20103 #2: Protein/peptide | Mass: 3641.135 Da / Num. of mol.: 2 / Mutation: S12C, S26(J9A), C30A, C34A / Source method: obtained synthetically / Source: (synth.) Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q7BB86, UniProt: P29559*PLUS #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: 2.8 Å3/Da / Density % sol: 56.14 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18.3% PEG 6000, 0.1 M bicine pH 8.0, 1 mM dithiothreitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→127.61 Å / Num. obs: 62069 / % possible obs: 93.1 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.79→2.89 Å / Rmerge(I) obs: 0.836 / Num. unique obs: 4205 / CC1/2: 0.867 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WD9 Resolution: 2.794→29.393 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.794→29.393 Å
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Refine LS restraints |
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LS refinement shell |
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