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- PDB-5nmn: Atomic resolution structure of LL-37 in a monomeric state -

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Basic information

Entry
Database: PDB / ID: 5nmn
TitleAtomic resolution structure of LL-37 in a monomeric state
ComponentsCathelicidin antimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide / cathelicidin / LL-37 / atomic resolution
Function / homology
Function and homology information


cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection ...cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection / lipopolysaccharide binding / specific granule lumen / positive regulation of angiogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / antibacterial humoral response / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of protein phosphorylation / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Cystatin superfamily
Similarity search - Domain/homology
Cathelicidin antimicrobial peptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å
AuthorsZeth, K. / Sancho-Vaello, E.
CitationJournal: Sci Rep / Year: 2017
Title: Structural remodeling and oligomerization of human cathelicidin on membranes suggest fibril-like structures as active species.
Authors: Sancho-Vaello, E. / Francois, P. / Bonetti, E.J. / Lilie, H. / Finger, S. / Gil-Ortiz, F. / Gil-Carton, D. / Zeth, K.
History
DepositionApr 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathelicidin antimicrobial peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5272
Polymers4,5041
Non-polymers231
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area3750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.381, 17.832, 34.032
Angle α, β, γ (deg.)90.00, 105.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Cathelicidin antimicrobial peptide / 18 kDa cationic antimicrobial protein / hCAP-18


Mass: 4504.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49913
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG3350, 100 mM Tris, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. obs: 99140 / % possible obs: 92.6 % / Redundancy: 4.75 % / CC1/2: 0.999 / Net I/σ(I): 16.18
Reflection shellResolution: 0.95→1.01 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 2853 / CC1/2: 0.917 / Rrim(I) all: 1.125 / % possible all: 79.2

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XSCALEdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.95→29.136 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.13
RfactorNum. reflection% reflection
Rfree0.1538 1034 5 %
Rwork0.1557 --
obs0.1555 20693 92.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.95→29.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms295 0 1 15 311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005336
X-RAY DIFFRACTIONf_angle_d0.92445
X-RAY DIFFRACTIONf_dihedral_angle_d10.017147
X-RAY DIFFRACTIONf_chiral_restr0.03645
X-RAY DIFFRACTIONf_plane_restr0.00457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-1.00010.3781200.37032297X-RAY DIFFRACTION77
1.0001-1.06280.20471450.20642731X-RAY DIFFRACTION90
1.0628-1.14480.1751450.13482789X-RAY DIFFRACTION93
1.1448-1.260.15131520.11562879X-RAY DIFFRACTION94
1.26-1.44230.13371530.11012908X-RAY DIFFRACTION96
1.4423-1.81720.13691560.13262958X-RAY DIFFRACTION97
1.8172-29.15010.15211630.16773097X-RAY DIFFRACTION98

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