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Yorodumi- PDB-7drm: Structure of ATP-grasp ligase PsnB complexed with minimal precurs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7drm | ||||||
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Title | Structure of ATP-grasp ligase PsnB complexed with minimal precursor, Mg, and ADP | ||||||
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: 3.28 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 | 7drm.cif.gz | 487.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7drm.ent.gz | 397.3 KB | Display | PDB format |
PDBx/mmJSON format | 7drm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7drm_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7drm_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7drm_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 7drm_validation.cif.gz | 59.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/7drm ftp://data.pdbj.org/pub/pdb/validation_reports/dr/7drm | HTTPS FTP |
-Related structure data
Related structure data | 7drnC 7droC 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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Unit cell |
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-Components
#1: Protein | Mass: 37023.816 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plesiocystis pacifica SIR-1 (bacteria) / Gene: PPSIR1_03893 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6G4D7 #2: Protein/peptide | Mass: 2567.886 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Plesiocystis pacifica SIR-1 (bacteria) / References: UniProt: A6GH40 #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.65 Å3/Da / Density % sol: 53.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: Sodium acetate, 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: Oct 18, 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: 3.28→32.83 Å / Num. obs: 25135 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 81.45 Å2 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.055 / Rrim(I) all: 0.15 / Χ2: 4.054 / Net I/σ(I): 10.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IG9 Resolution: 3.28→32.83 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.99 / 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: 193.51 Å2 / Biso mean: 93.2775 Å2 / Biso min: 40.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.28→32.83 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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