+Open data
-Basic information
Entry | Database: PDB / ID: 3njw | ||||||
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Title | First High Resolution Crystal Structure of a Lasso Peptide | ||||||
Components | Bicyclic peptide BI-32169 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / lasso peptide / lariat / protoknot / BI-32169 / glucagon receptor antagonist / microbial peptide | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 0.86 Å | ||||||
Authors | Nar, H. / Schmid, A. / Puder, C. / Potterat, O. | ||||||
Citation | Journal: Chemmedchem / Year: 2010 Title: High-resolution crystal structure of a lasso Peptide. Authors: Nar, H. / Schmid, A. / Puder, C. / Potterat, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3njw.cif.gz | 14.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3njw.ent.gz | 10.3 KB | Display | PDB format |
PDBx/mmJSON format | 3njw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/3njw ftp://data.pdbj.org/pub/pdb/validation_reports/nj/3njw | HTTPS FTP |
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-Related structure data
Similar structure data |
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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 | Mass: 2057.310 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: DSM 14996 / Production host: Streptomyces sp. (bacteria) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.5 Å3/Da / Density % sol: 17.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: BI-32169 peptide in 50% DMSO/water mixture equilibrated against 20-50% MPD, 0.1-0.5M sodium phosphate or ammonium sulphate, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 25, 2006 / Details: multilayer optics |
Radiation | Monochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 0.86→8.94 Å / Num. all: 19700 / Num. obs: 19602 / % possible obs: 98.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 16 |
Reflection shell | Resolution: 0.86→0.9 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.1 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 0.86→8.94 Å / Num. parameters: 1443 / Num. restraintsaints: 0 / Cross valid method: THROUGHOUT / σ(F): 4
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 124 / Occupancy sum non hydrogen: 161 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.86→8.94 Å
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LS refinement shell | Highest resolution: 0.86 Å / Num. reflection obs: 16628 |