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- PDB-5nnm: The crystal structure of dimeric LL-37 -

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Basic information

Entry
Database: PDB / ID: 5nnm
TitleThe crystal structure of dimeric LL-37
ComponentsCathelicidin antimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN / AMP / LL-37 / LDAO / peptide-detergent complex / antimicrobial peptide
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 / cellular response to tumor necrosis factor / antibacterial humoral response / 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) / Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cystatin superfamily
Similarity search - Domain/homology
CARBONATE ION / Cathelicidin antimicrobial peptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.9 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 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathelicidin antimicrobial peptide
B: Cathelicidin antimicrobial peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2496
Polymers9,0092
Non-polymers2404
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-12 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.577, 44.577, 87.847
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 1 - 31 / Label seq-ID: 1 - 31

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein/peptide Cathelicidin antimicrobial peptide / 18 kDa cationic antimicrobial protein / hCAP-18 / Cathelicidin LL-37


Mass: 4504.351 Da / Num. of mol.: 2 / Fragment: UNP Residues 134-170 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49913
#2: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 15% Peg400, 0.1 M 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 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.35
11-h,-k,l20.65
ReflectionResolution: 1.9→40 Å / Num. obs: 10991 / % possible obs: 99.2 % / Redundancy: 3.5 % / Net I/σ(I): 7.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.9→38.6 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.802 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25101 389 5.2 %RANDOM
Rwork0.2231 ---
obs0.22473 7055 88.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms572 0 16 23 611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0390.019621
X-RAY DIFFRACTIONr_bond_other_d0.0070.02674
X-RAY DIFFRACTIONr_angle_refined_deg2.9462.01816
X-RAY DIFFRACTIONr_angle_other_deg1.93731543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.77520.32331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.18315144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.161511
X-RAY DIFFRACTIONr_chiral_restr0.1260.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02660
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02159
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1984.338272
X-RAY DIFFRACTIONr_mcbond_other5.2034.33271
X-RAY DIFFRACTIONr_mcangle_it7.2916.401338
X-RAY DIFFRACTIONr_mcangle_other7.2846.409339
X-RAY DIFFRACTIONr_scbond_it6.6385.284349
X-RAY DIFFRACTIONr_scbond_other6.5825.251338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.6167.514464
X-RAY DIFFRACTIONr_long_range_B_refined12.89139.9821851
X-RAY DIFFRACTIONr_long_range_B_other12.86239.9661847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3010 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 23 -
Rwork0.329 602 -
obs--98.43 %

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