+Open data
-Basic information
Entry | Database: PDB / ID: 8u78 | |||||||||
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Title | Structure of a N-Me-D-Gln4,Lys10-teixobactin analogue | |||||||||
Components | N-Methyl-D-Gln4,Lys10-teixobactin | |||||||||
Keywords | ANTIBIOTIC / teixobactin / teixobactin analogue | |||||||||
Function / homology | : / Chem-PG6 Function and homology information | |||||||||
Biological species | Eleftheria terrae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | |||||||||
Authors | Nowick, J.S. / Yang, H. / Kreutzer, A.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Org.Chem. / Year: 2024 Title: Supramolecular Interactions of Teixobactin Analogues in the Crystal State. Authors: Yang, H. / Kreutzer, A.G. / 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 | 8u78.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u78.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 8u78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u78_validation.pdf.gz | 619.8 KB | Display | wwPDB validaton report |
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Full document | 8u78_full_validation.pdf.gz | 624.9 KB | Display | |
Data in XML | 8u78_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 8u78_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/8u78 ftp://data.pdbj.org/pub/pdb/validation_reports/u7/8u78 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Type: Peptide-like / Class: Antibiotic / Mass: 1249.520 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Eleftheria terrae (bacteria) / References: BIRD: PRD_002532 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-PG6 / | #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: 1.65 Å3/Da / Density % sol: 25.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG3350, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99997 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→24.88 Å / Num. obs: 10322 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 14.35 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01774 / Rpim(I) all: 0.01774 / Rrim(I) all: 0.02509 / Net I/σ(I): 24.09 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1934 / Mean I/σ(I) obs: 4.24 / Num. unique obs: 1055 / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.1934 / Rrim(I) all: 0.2735 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→24.88 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 22.71 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→24.88 Å
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Refine LS restraints |
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LS refinement shell |
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