+Open data
-Basic information
Entry | Database: PDB / ID: 8cuf | |||||||||
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Title | Synthetic epi-Novo29 (2R,3S), X-ray diffractometer structure | |||||||||
Components | Synthetic epi-Novo29 (2R,3S) | |||||||||
Keywords | ANTIBIOTIC / macrocyclic peptide | |||||||||
Function / homology | ACETATE ION / IODIDE ION Function and homology information | |||||||||
Biological species | Eleftheria (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.68 Å | |||||||||
Authors | Kreutzer, A.G. / Li, X. / Krumberger, M. / Nowick, J.S. | |||||||||
Funding support | 1items
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Citation | Journal: J.Org.Chem. / Year: 2023 Title: Synthesis and Stereochemical Determination of the Peptide Antibiotic Novo29. Authors: Krumberger, M. / Li, X. / Kreutzer, A.G. / Peoples, A.J. / Nitti, A.G. / Cunningham, A.M. / Jones, C.R. / Achorn, C. / Ling, L.L. / Hughes, D.E. / Nowick, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cuf.cif.gz | 17 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cuf.ent.gz | 10.3 KB | Display | PDB format |
PDBx/mmJSON format | 8cuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/8cuf ftp://data.pdbj.org/pub/pdb/validation_reports/cu/8cuf | HTTPS FTP |
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-Related structure data
Related structure data | 8cugC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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/peptide | Mass: 921.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Eleftheria (bacteria) #2: Chemical | ChemComp-ACT / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.92 Å3/Da / Density % sol: 35.79 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 2.8 M sodium acetate trihydrate, pH 6.6 |
-Data collection
Diffraction | Mean temperature: 123.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→24 Å / Num. obs: 2869 / % possible obs: 95.61 % / Redundancy: 13.1 % / CC1/2: 0.869 / Net I/σ(I): 36.1 |
Reflection shell | Resolution: 1.68→1.74 Å / Num. unique obs: 111 / CC1/2: 0.822 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.68→24 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 11.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 46.92 Å2 / Biso mean: 10.8764 Å2 / Biso min: 1.21 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→24 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
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