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Yorodumi- PDB-7dro: Structure of ATP-grasp ligase PsnB complexed with minimal precursor -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dro | ||||||
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Title | Structure of ATP-grasp ligase PsnB complexed with minimal precursor | ||||||
Components |
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Keywords | LIGASE / ATP-grasp ligase / RiPP / graspetide / Omega ester bond containing peptide | ||||||
Function / homology | Function and homology information N-acetyl-L-aspartate-L-glutamate ligase activity / ribosomal S6-glutamic acid ligase activity / SOS response / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plesiocystis pacifica SIR-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Song, I. / Yu, J. / Song, W. / Kim, S. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: Molecular mechanism underlying substrate recognition of the peptide macrocyclase PsnB. Authors: Song, I. / Kim, Y. / Yu, J. / Go, S.Y. / Lee, H.G. / Song, W.J. / Kim, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dro.cif.gz | 659.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dro.ent.gz | 547.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dro_validation.pdf.gz | 512.9 KB | Display | wwPDB validaton report |
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Full document | 7dro_full_validation.pdf.gz | 531.6 KB | Display | |
Data in XML | 7dro_validation.xml.gz | 59.3 KB | Display | |
Data in CIF | 7dro_validation.cif.gz | 80.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/7dro ftp://data.pdbj.org/pub/pdb/validation_reports/dr/7dro | HTTPS FTP |
-Related structure data
Related structure data | 7drmC 7drnC 7drpC 5ig9S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37023.816 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plesiocystis pacifica SIR-1 (bacteria) / Gene: PPSIR1_03893 / Production host: Escherichia coli (E. coli) / References: UniProt: A6G4D7 #2: Protein/peptide | Mass: 2567.886 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Plesiocystis pacifica SIR-1 (bacteria) / References: UniProt: A6GH40 |
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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: 2.31 Å3/Da / Density % sol: 46.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: Tacsimate, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 2, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.25→47.04 Å / Num. obs: 34587 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 80.55 Å2 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.042 / Rrim(I) all: 0.161 / Χ2: 6.643 / Net I/σ(I): 8.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ig9 Resolution: 3.25→47.04 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.57 Å2 / Biso mean: 79.639 Å2 / Biso min: 30.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.25→47.04 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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