+Open data
-Basic information
Entry | Database: PDB / ID: 1lxe | ||||||
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Title | CRYSTAL STRUCTURE OF THE CATHELICIDIN MOTIF OF PROTEGRINS | ||||||
Components | protegrin-3 precursor | ||||||
Keywords | ANTIMICROBIAL PROTEIN / PROTEGRIN / CATHELICIDIN MOTIF / DISULFIDE / domain swapping | ||||||
Function / homology | Function and homology information lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / innate immune response / extracellular space Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Sanchez, J.F. / Hoh, F. / Strub, M.P. / Aumelas, A. / Dumas, C. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structure of the cathelicidin motif of protegrin-3 precursor: structural insights into the activation mechanism of an antimicrobial protein. Authors: Sanchez, J.F. / Hoh, F. / Strub, M.P. / Aumelas, A. / Dumas, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lxe.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lxe.ent.gz | 20.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lxe_validation.pdf.gz | 423.3 KB | Display | wwPDB validaton report |
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Full document | 1lxe_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 1lxe_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1lxe_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/1lxe ftp://data.pdbj.org/pub/pdb/validation_reports/lx/1lxe | HTTPS FTP |
-Related structure data
Related structure data | 1kwiSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: Rotation : 0.5000 0.8660 0.0 0.8660 -0.5000 0.0 0.0 0.0 -1.0 Translation : -26.086 45.183 -22.580 |
-Components
#1: Protein | Mass: 11322.741 Da / Num. of mol.: 1 / Fragment: residues 30-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: pg3 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P32196 |
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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: 2.35 Å3/Da / Density % sol: 47.62 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: AMMONIUM SULFATE, SODIUM ACETATE, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / PH range low: 3.7 / PH range high: 3.5 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→27.1 Å / Num. all: 3922 / Num. obs: 3922 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.5→2.66 Å / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 4.6 / Num. unique all: 541 / Rsym value: 0.241 / % possible all: 91.3 |
Reflection | *PLUS % possible obs: 93.3 % / Num. measured all: 37505 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1KWI Resolution: 2.5→27.1 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1799954.7 / Data cutoff high rms absF: 1799954.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 104.394 Å2 / ksol: 0.429523 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→27.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 27.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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