+Open data
-Basic information
Entry | Database: PDB / ID: 5jqf | |||||||||
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Title | Crystal structure of the lasso peptide Sphingopyxin I (SpI) | |||||||||
Components | Sphingopyxin I | |||||||||
Keywords | UNKNOWN FUNCTION / Lasso peptide / isopeptide bond / macrolactam ring | |||||||||
Function / homology | Sphingopyxin I Function and homology information | |||||||||
Biological species | Sphingopyxis alaskensis RB2256 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.85 Å | |||||||||
Authors | Fage, C.D. / Hegemann, J.D. / Harms, K. / Bange, G. / Marahiel, M.A. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2016 Title: Structure and Mechanism of the Sphingopyxin I Lasso Peptide Isopeptidase. Authors: Fage, C.D. / Hegemann, J.D. / Nebel, A.J. / Steinbach, R.M. / Zhu, S. / Linne, U. / Harms, K. / Bange, G. / Marahiel, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jqf.cif.gz | 40 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jqf.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jqf_validation.pdf.gz | 293.2 KB | Display | wwPDB validaton report |
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Full document | 5jqf_full_validation.pdf.gz | 293.2 KB | Display | |
Data in XML | 5jqf_validation.xml.gz | 4 KB | Display | |
Data in CIF | 5jqf_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/5jqf ftp://data.pdbj.org/pub/pdb/validation_reports/jq/5jqf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein/peptide | Mass: 2201.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: An isopeptide bond exists between the N-terminus of Gly1 and side chain of Asp9 Source: (gene. exp.) Sphingopyxis alaskensis RB2256 (bacteria) Plasmid: pET41a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D5B387*PLUS #2: Water | ChemComp-HOH / | |
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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: 1.59 Å3/Da / Density % sol: 22.43 % / Description: Needle-like |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M K2SO4, 20%(w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.82656 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.82656 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.85→50 Å / Num. obs: 24225 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 8.602 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.01 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.85→33.98 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.358 / SU ML: 0.01 / SU R Cruickshank DPI: 0.0154 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.015 / ESU R Free: 0.017 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.7 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 25.23 Å2 / Biso mean: 6.914 Å2 / Biso min: 3.57 Å2
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Refinement step | Cycle: final / Resolution: 0.85→33.98 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1806 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.21 Å / Weight position: 0.05
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LS refinement shell | Resolution: 0.85→0.896 Å / Total num. of bins used: 10
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