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Yorodumi- PDB-5xhb: Crystal structure of the full length of NisI in a lipid free form... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xhb | ||||||
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Title | Crystal structure of the full length of NisI in a lipid free form, the nisin immunity protein, from Lactococcus lactis | ||||||
Components | Nisin immunity protein | ||||||
Keywords | IMMUNE SYSTEM / Immunity protein | ||||||
Function / homology | Lantibiotic immunity protein Spa1, C-terminal / Lantibiotic immunity protein Spa1 C-terminal domain / bacteriocin immunity / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / Nisin immunity protein Function and homology information | ||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ha, S.C. | ||||||
Citation | Journal: Antimicrob. Agents Chemother. / Year: 2018 Title: Crystal Structure of NisI in a Lipid-Free Form, the Nisin Immunity Protein, from Lactococcus lactis Authors: Jeong, J.H. / Ha, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xhb.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xhb.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 5xhb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xhb_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 5xhb_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 5xhb_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 5xhb_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/5xhb ftp://data.pdbj.org/pub/pdb/validation_reports/xh/5xhb | HTTPS FTP |
-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 | Mass: 26318.584 Da / Num. of mol.: 1 / Fragment: UNP residues 22-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Gene: nisI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42708 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 30-40mM ammonium sulfate, 0.1M Na-acetate pH 4.6, 16-18% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97917 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 3, 2015 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 21483 / % possible obs: 98.3 % / Redundancy: 13.2 % / Net I/σ(I): 11.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.444 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.73 / Phase error: 19.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.444 Å
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Refine LS restraints |
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LS refinement shell |
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