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- PDB-6s6n: Crystal structure of the Gorilla LL37(17-29) antimicrobial peptide -

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Basic information

Entry
Database: PDB / ID: 6s6n
TitleCrystal structure of the Gorilla LL37(17-29) antimicrobial peptide
ComponentsCathelicidin antimicrobial peptide
KeywordsPROTEIN FIBRIL / Helical and tubular fibril structure of a gorilla derived antimicrobial peptide
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
Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like
Similarity search - Domain/homology
Cathelicidin antimicrobial peptide
Similarity search - Component
Biological speciesGorilla gorilla gorilla (western lowland gorilla)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
Model detailsAntimicrobial
AuthorsLandau, M. / Engelberg, Y.
CitationJournal: Nat Commun / Year: 2020
Title: The Human LL-37(17-29) antimicrobial peptide reveals a functional supramolecular structure.
Authors: Engelberg, Y. / Landau, M.
History
DepositionJul 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)3,3282
Polymers3,3282
Non-polymers00
Water1,00956
1
A: Cathelicidin antimicrobial peptide
x 180
B: Cathelicidin antimicrobial peptide
x 180


Theoretical massNumber of molelcules
Total (without water)599,050360
Polymers599,050360
Non-polymers00
Water6,485360
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation1_554x,y,z-12
crystal symmetry operation1_553x,y,z-22
crystal symmetry operation1_552x,y,z-32
crystal symmetry operation1_551x,y,z-42
crystal symmetry operation1_665x+1,y+1,z2
crystal symmetry operation1_664x+1,y+1,z-12
crystal symmetry operation1_663x+1,y+1,z-22
crystal symmetry operation1_662x+1,y+1,z-32
crystal symmetry operation1_661x+1,y+1,z-42
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_654x+1,y,z-11
crystal symmetry operation1_653x+1,y,z-21
crystal symmetry operation1_652x+1,y,z-31
crystal symmetry operation1_651x+1,y,z-41
crystal symmetry operation2_555-y,x-y,z+1/32
crystal symmetry operation2_554-y,x-y,z-2/32
crystal symmetry operation2_553-y,x-y,z-5/32
crystal symmetry operation2_552-y,x-y,z-8/32
crystal symmetry operation2_551-y,x-y,z-11/32
crystal symmetry operation2_455-y-1,x-y,z+1/32
crystal symmetry operation2_454-y-1,x-y,z-2/32
crystal symmetry operation2_453-y-1,x-y,z-5/32
crystal symmetry operation2_452-y-1,x-y,z-8/32
crystal symmetry operation2_451-y-1,x-y,z-11/32
crystal symmetry operation2_565-y,x-y+1,z+1/31
crystal symmetry operation2_564-y,x-y+1,z-2/31
crystal symmetry operation2_563-y,x-y+1,z-5/31
crystal symmetry operation2_562-y,x-y+1,z-8/31
crystal symmetry operation2_561-y,x-y+1,z-11/31
crystal symmetry operation3_555-x+y,-x,z+2/32
crystal symmetry operation3_554-x+y,-x,z-1/32
crystal symmetry operation3_553-x+y,-x,z-4/32
crystal symmetry operation3_552-x+y,-x,z-7/32
crystal symmetry operation3_551-x+y,-x,z-10/32
crystal symmetry operation3_545-x+y,-x-1,z+2/32
crystal symmetry operation3_544-x+y,-x-1,z-1/32
crystal symmetry operation3_543-x+y,-x-1,z-4/32
crystal symmetry operation3_542-x+y,-x-1,z-7/32
crystal symmetry operation3_541-x+y,-x-1,z-10/32
crystal symmetry operation3_445-x+y-1,-x-1,z+2/31
crystal symmetry operation3_444-x+y-1,-x-1,z-1/31
crystal symmetry operation3_443-x+y-1,-x-1,z-4/31
crystal symmetry operation3_442-x+y-1,-x-1,z-7/31
crystal symmetry operation3_441-x+y-1,-x-1,z-10/31
crystal symmetry operation4_555-x,-y,z+1/22
crystal symmetry operation4_554-x,-y,z-1/22
crystal symmetry operation4_553-x,-y,z-3/22
crystal symmetry operation4_552-x,-y,z-5/22
crystal symmetry operation4_551-x,-y,z-7/22
crystal symmetry operation4_445-x-1,-y-1,z+1/22
crystal symmetry operation4_444-x-1,-y-1,z-1/22
crystal symmetry operation4_443-x-1,-y-1,z-3/22
crystal symmetry operation4_442-x-1,-y-1,z-5/22
crystal symmetry operation4_441-x-1,-y-1,z-7/22
crystal symmetry operation4_455-x-1,-y,z+1/21
crystal symmetry operation4_454-x-1,-y,z-1/21
crystal symmetry operation4_453-x-1,-y,z-3/21
crystal symmetry operation4_452-x-1,-y,z-5/21
crystal symmetry operation4_451-x-1,-y,z-7/21
crystal symmetry operation5_555y,-x+y,z+5/62
crystal symmetry operation5_554y,-x+y,z-1/62
crystal symmetry operation5_553y,-x+y,z-7/62
crystal symmetry operation5_552y,-x+y,z-13/62
crystal symmetry operation5_551y,-x+y,z-19/62
crystal symmetry operation5_655y+1,-x+y,z+5/62
crystal symmetry operation5_654y+1,-x+y,z-1/62
crystal symmetry operation5_653y+1,-x+y,z-7/62
crystal symmetry operation5_652y+1,-x+y,z-13/62
crystal symmetry operation5_651y+1,-x+y,z-19/62
crystal symmetry operation5_545y,-x+y-1,z+5/61
crystal symmetry operation5_544y,-x+y-1,z-1/61
crystal symmetry operation5_543y,-x+y-1,z-7/61
crystal symmetry operation5_542y,-x+y-1,z-13/61
crystal symmetry operation5_541y,-x+y-1,z-19/61
crystal symmetry operation6_555x-y,x,z+1/62
crystal symmetry operation6_554x-y,x,z-5/62
crystal symmetry operation6_553x-y,x,z-11/62
crystal symmetry operation6_552x-y,x,z-17/62
crystal symmetry operation6_551x-y,x,z-23/62
crystal symmetry operation6_565x-y,x+1,z+1/62
crystal symmetry operation6_564x-y,x+1,z-5/62
crystal symmetry operation6_563x-y,x+1,z-11/62
crystal symmetry operation6_562x-y,x+1,z-17/62
crystal symmetry operation6_561x-y,x+1,z-23/62
crystal symmetry operation6_665x-y+1,x+1,z+1/61
crystal symmetry operation6_664x-y+1,x+1,z-5/61
crystal symmetry operation6_663x-y+1,x+1,z-11/61
crystal symmetry operation6_662x-y+1,x+1,z-17/61
crystal symmetry operation6_661x-y+1,x+1,z-23/61
crystal symmetry operation7_555y,x,-z+1/32
crystal symmetry operation7_554y,x,-z-2/32
crystal symmetry operation7_553y,x,-z-5/32
crystal symmetry operation7_552y,x,-z-8/32
crystal symmetry operation7_551y,x,-z-11/32
crystal symmetry operation7_665y+1,x+1,-z+1/32
crystal symmetry operation7_664y+1,x+1,-z-2/32
crystal symmetry operation7_663y+1,x+1,-z-5/32
crystal symmetry operation7_662y+1,x+1,-z-8/32
crystal symmetry operation7_661y+1,x+1,-z-11/32
crystal symmetry operation7_565y,x+1,-z+1/31
crystal symmetry operation7_564y,x+1,-z-2/31
crystal symmetry operation7_563y,x+1,-z-5/31
crystal symmetry operation7_562y,x+1,-z-8/31
crystal symmetry operation7_561y,x+1,-z-11/31
crystal symmetry operation8_555x-y,-y,-z2
crystal symmetry operation8_554x-y,-y,-z-12
crystal symmetry operation8_553x-y,-y,-z-22
crystal symmetry operation8_552x-y,-y,-z-32
crystal symmetry operation8_551x-y,-y,-z-42
crystal symmetry operation8_545x-y,-y-1,-z2
crystal symmetry operation8_544x-y,-y-1,-z-12
crystal symmetry operation8_543x-y,-y-1,-z-22
crystal symmetry operation8_542x-y,-y-1,-z-32
crystal symmetry operation8_541x-y,-y-1,-z-42
crystal symmetry operation8_655x-y+1,-y,-z1
crystal symmetry operation8_654x-y+1,-y,-z-11
crystal symmetry operation8_653x-y+1,-y,-z-21
crystal symmetry operation8_652x-y+1,-y,-z-31
crystal symmetry operation8_651x-y+1,-y,-z-41
crystal symmetry operation9_555-x,-x+y,-z+2/32
crystal symmetry operation9_554-x,-x+y,-z-1/32
crystal symmetry operation9_553-x,-x+y,-z-4/32
crystal symmetry operation9_552-x,-x+y,-z-7/32
crystal symmetry operation9_551-x,-x+y,-z-10/32
crystal symmetry operation9_455-x-1,-x+y,-z+2/32
crystal symmetry operation9_454-x-1,-x+y,-z-1/32
crystal symmetry operation9_453-x-1,-x+y,-z-4/32
crystal symmetry operation9_452-x-1,-x+y,-z-7/32
crystal symmetry operation9_451-x-1,-x+y,-z-10/32
crystal symmetry operation9_445-x-1,-x+y-1,-z+2/31
crystal symmetry operation9_444-x-1,-x+y-1,-z-1/31
crystal symmetry operation9_443-x-1,-x+y-1,-z-4/31
crystal symmetry operation9_442-x-1,-x+y-1,-z-7/31
crystal symmetry operation9_441-x-1,-x+y-1,-z-10/31
crystal symmetry operation10_555-y,-x,-z+5/62
crystal symmetry operation10_554-y,-x,-z-1/62
crystal symmetry operation10_553-y,-x,-z-7/62
crystal symmetry operation10_552-y,-x,-z-13/62
crystal symmetry operation10_551-y,-x,-z-19/62
crystal symmetry operation10_445-y-1,-x-1,-z+5/62
crystal symmetry operation10_444-y-1,-x-1,-z-1/62
crystal symmetry operation10_443-y-1,-x-1,-z-7/62
crystal symmetry operation10_442-y-1,-x-1,-z-13/62
crystal symmetry operation10_441-y-1,-x-1,-z-19/62
crystal symmetry operation10_545-y,-x-1,-z+5/61
crystal symmetry operation10_544-y,-x-1,-z-1/61
crystal symmetry operation10_543-y,-x-1,-z-7/61
crystal symmetry operation10_542-y,-x-1,-z-13/61
crystal symmetry operation10_541-y,-x-1,-z-19/61
crystal symmetry operation11_555-x+y,y,-z+1/22
crystal symmetry operation11_554-x+y,y,-z-1/22
crystal symmetry operation11_553-x+y,y,-z-3/22
crystal symmetry operation11_552-x+y,y,-z-5/22
crystal symmetry operation11_551-x+y,y,-z-7/22
crystal symmetry operation11_565-x+y,y+1,-z+1/22
crystal symmetry operation11_564-x+y,y+1,-z-1/22
crystal symmetry operation11_563-x+y,y+1,-z-3/22
crystal symmetry operation11_562-x+y,y+1,-z-5/22
crystal symmetry operation11_561-x+y,y+1,-z-7/22
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation11_453-x+y-1,y,-z-3/21
crystal symmetry operation11_452-x+y-1,y,-z-5/21
crystal symmetry operation11_451-x+y-1,y,-z-7/21
crystal symmetry operation12_555x,x-y,-z+1/62
crystal symmetry operation12_554x,x-y,-z-5/62
crystal symmetry operation12_553x,x-y,-z-11/62
crystal symmetry operation12_552x,x-y,-z-17/62
crystal symmetry operation12_551x,x-y,-z-23/62
crystal symmetry operation12_655x+1,x-y,-z+1/62
crystal symmetry operation12_654x+1,x-y,-z-5/62
crystal symmetry operation12_653x+1,x-y,-z-11/62
crystal symmetry operation12_652x+1,x-y,-z-17/62
crystal symmetry operation12_651x+1,x-y,-z-23/62
crystal symmetry operation12_665x+1,x-y+1,-z+1/61
crystal symmetry operation12_664x+1,x-y+1,-z-5/61
crystal symmetry operation12_663x+1,x-y+1,-z-11/61
crystal symmetry operation12_662x+1,x-y+1,-z-17/61
crystal symmetry operation12_661x+1,x-y+1,-z-23/61
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_564x,y+1,z-11
crystal symmetry operation1_563x,y+1,z-21
crystal symmetry operation1_562x,y+1,z-31
crystal symmetry operation1_561x,y+1,z-41
crystal symmetry operation2_445-y-1,x-y-1,z+1/31
crystal symmetry operation2_444-y-1,x-y-1,z-2/31
crystal symmetry operation2_443-y-1,x-y-1,z-5/31
crystal symmetry operation2_442-y-1,x-y-1,z-8/31
crystal symmetry operation2_441-y-1,x-y-1,z-11/31
crystal symmetry operation3_655-x+y+1,-x,z+2/31
crystal symmetry operation3_654-x+y+1,-x,z-1/31
crystal symmetry operation3_653-x+y+1,-x,z-4/31
crystal symmetry operation3_652-x+y+1,-x,z-7/31
crystal symmetry operation3_651-x+y+1,-x,z-10/31
crystal symmetry operation4_545-x,-y-1,z+1/21
crystal symmetry operation4_544-x,-y-1,z-1/21
crystal symmetry operation4_543-x,-y-1,z-3/21
crystal symmetry operation4_542-x,-y-1,z-5/21
crystal symmetry operation4_541-x,-y-1,z-7/21
crystal symmetry operation5_665y+1,-x+y+1,z+5/61
crystal symmetry operation5_664y+1,-x+y+1,z-1/61
crystal symmetry operation5_663y+1,-x+y+1,z-7/61
crystal symmetry operation5_662y+1,-x+y+1,z-13/61
crystal symmetry operation5_661y+1,-x+y+1,z-19/61
crystal symmetry operation6_455x-y-1,x,z+1/61
crystal symmetry operation6_454x-y-1,x,z-5/61
crystal symmetry operation6_453x-y-1,x,z-11/61
crystal symmetry operation6_452x-y-1,x,z-17/61
crystal symmetry operation6_451x-y-1,x,z-23/61
crystal symmetry operation7_655y+1,x,-z+1/31
crystal symmetry operation7_654y+1,x,-z-2/31
crystal symmetry operation7_653y+1,x,-z-5/31
crystal symmetry operation7_652y+1,x,-z-8/31
crystal symmetry operation7_651y+1,x,-z-11/31
crystal symmetry operation8_445x-y-1,-y-1,-z1
crystal symmetry operation8_444x-y-1,-y-1,-z-11
crystal symmetry operation8_443x-y-1,-y-1,-z-21
crystal symmetry operation8_442x-y-1,-y-1,-z-31
crystal symmetry operation8_441x-y-1,-y-1,-z-41
crystal symmetry operation9_565-x,-x+y+1,-z+2/31
crystal symmetry operation9_564-x,-x+y+1,-z-1/31
crystal symmetry operation9_563-x,-x+y+1,-z-4/31
crystal symmetry operation9_562-x,-x+y+1,-z-7/31
crystal symmetry operation9_561-x,-x+y+1,-z-10/31
crystal symmetry operation10_455-y-1,-x,-z+5/61
crystal symmetry operation10_454-y-1,-x,-z-1/61
crystal symmetry operation10_453-y-1,-x,-z-7/61
crystal symmetry operation10_452-y-1,-x,-z-13/61
crystal symmetry operation10_451-y-1,-x,-z-19/61
crystal symmetry operation11_665-x+y+1,y+1,-z+1/21
crystal symmetry operation11_664-x+y+1,y+1,-z-1/21
crystal symmetry operation11_663-x+y+1,y+1,-z-3/21
crystal symmetry operation11_662-x+y+1,y+1,-z-5/21
crystal symmetry operation11_661-x+y+1,y+1,-z-7/21
crystal symmetry operation12_545x,x-y-1,-z+1/61
crystal symmetry operation12_544x,x-y-1,-z-5/61
crystal symmetry operation12_543x,x-y-1,-z-11/61
crystal symmetry operation12_542x,x-y-1,-z-17/61
crystal symmetry operation12_541x,x-y-1,-z-23/61
Unit cell
Length a, b, c (Å)41.150, 41.150, 57.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-120-

HOH

21B-122-

HOH

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Components

#1: Protein/peptide Cathelicidin antimicrobial peptide


Mass: 1664.028 Da / Num. of mol.: 2
Fragment: Antimicrobial core segment of gorilla LL37 (residues 17-29)
Source method: obtained synthetically / Details: Gorilla LL37(17-29), synthesized
Source: (synth.) Gorilla gorilla gorilla (western lowland gorilla)
References: UniProt: Q1KLY3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.1 M HEPES pH 7.5, 1.4 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.1→35.64 Å / Num. obs: 12186 / % possible obs: 99.4 % / Redundancy: 18.242 % / Biso Wilson estimate: 13.999 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.057 / Χ2: 0.994 / Net I/σ(I): 31.12 / Num. measured all: 222293
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.136.4330.5523.1451988778080.9040.59892.1
1.13-1.168.8730.3935.5575868578550.9670.41899.8
1.16-1.1910.9540.3048.4892018408400.9850.319100
1.19-1.2313.0560.24811.73105628098090.9920.259100
1.23-1.2716.3620.24114.27129267907900.9940.249100
1.27-1.3120.480.2217.08155857617610.9970.225100
1.31-1.3622.7290.20120.28170927527520.9980.206100
1.36-1.4222.760.17222.57163197177170.9980.176100
1.42-1.4822.9470.1328.47156966846840.9990.133100
1.48-1.5523.0150.135.38152136616610.9990.102100
1.55-1.6422.70.07942.58144606376370.9990.081100
1.64-1.7422.4350.07543.35134616006000.9990.076100
1.74-1.8622.2970.0747.72126205665660.9990.072100
1.86-2.0121.8580.05654.95115855315300.9990.05899.8
2.01-2.221.9820.04763.351083749349310.048100
2.2-2.4621.8730.04367.6899964574570.9990.044100
2.46-2.8421.0650.04170.0884894034030.9990.042100
2.84-3.4718.7890.0469.22667035535510.041100
3.47-4.9120.2220.0473.2357432842840.9990.041100
4.91-35.6416.5980.04263.4630541841840.9980.044100

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0253refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly Ala alpha-helix

Resolution: 1.1→35.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.759 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.034
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1788 1219 10 %RANDOM
Rwork0.1595 ---
obs0.1613 10967 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 149.39 Å2 / Biso mean: 12.505 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 1.1→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms234 0 0 56 290
Biso mean---27.27 -
Num. residues----26
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013254
X-RAY DIFFRACTIONr_bond_other_d0.0020.018284
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.689337
X-RAY DIFFRACTIONr_angle_other_deg1.5281.638653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.214530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.5771720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9291565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.917156
X-RAY DIFFRACTIONr_chiral_restr0.0990.233
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0267
X-RAY DIFFRACTIONr_rigid_bond_restr1.7313538
LS refinement shellResolution: 1.1→1.127 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.559 81 -
Rwork0.478 727 -
obs--92.13 %

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