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- PDB-7npq: Crystal structure of the human LL37(17-29) I24C mutant antimicrob... -

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Basic information

Entry
Database: PDB / ID: 7npq
TitleCrystal structure of the human LL37(17-29) I24C mutant antimicrobial peptide
ComponentsCathelicidin antimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN / LL-37 / functional fibril / helical fibril / AMPs / cys mutant / design / 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
Cathelicidin antimicrobial peptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
Model detailsAntimicrobial
AuthorsLandau, M. / Engelberg, Y.
CitationJournal: Biomacromolecules / Year: 2022
Title: Rare by Natural Selection: Disulfide-Bonded Supramolecular Antimicrobial Peptides.
Authors: Engelberg, Y. / Ragonis-Bachar, P. / Landau, M.
History
DepositionFeb 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,4282
Polymers3,4282
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-10 kcal/mol
Surface area3200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.920, 34.920, 44.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-109-

HOH

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Components

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


Mass: 1714.109 Da / Num. of mol.: 2
Fragment: Antimicrobial core segment of human LL37 (residues 17-29) I8C mutant
Source method: obtained synthetically / Details: Human LL-37(17-29) I24C mutant, synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P49913
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The LL-37(17-29) I24C peptide was mixed with 0.1mM DTT in water: Reservoir contained 2.8 M sodium acetate trihydrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→27.49 Å / Num. obs: 4721 / % possible obs: 99 % / Redundancy: 7.571 % / Biso Wilson estimate: 29.339 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.056 / Χ2: 1.042 / Net I/σ(I): 19.87 / Num. measured all: 35742
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
1.5-1.553.7730.6582.1714454213830.6990.75191
1.55-1.66.3280.5214.3924113823810.880.56799.7
1.6-1.78.1530.3866.8352106396390.9530.413100
1.7-1.88.2620.23510.3841315005000.9890.251100
1.8-2.18.320.1117.988345100310030.9970.117100
2.1-2.58.1340.06130.6658087157140.9960.06599.9
2.5-37.9550.04735.8735404454450.9980.05100
3-4.57.8120.04240.2434924474470.9990.045100
4.5-106.8180.03438.6212751901870.9970.03798.4
10-27.493.8640.01828.9685252210.0288

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBid 6S6M with residues mutated to alanine

6s6m


Resolution: 1.5→27.49 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1948 / WRfactor Rwork: 0.1894 / FOM work R set: 0.8614 / SU B: 1.354 / SU ML: 0.049 / SU R Cruickshank DPI: 0.082 / SU Rfree: 0.0757 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 472 10 %RANDOM
Rwork0.1789 ---
obs0.1803 4249 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83 Å2 / Biso mean: 28.058 Å2 / Biso min: 15.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.5→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms240 0 0 16 256
Biso mean---39.54 -
Num. residues----26
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013262
X-RAY DIFFRACTIONr_bond_other_d0.0020.018289
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.702344
X-RAY DIFFRACTIONr_angle_other_deg1.4841.641655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.171527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.50715.45522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.691563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.453157
X-RAY DIFFRACTIONr_chiral_restr0.1160.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02285
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0285
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 29 -
Rwork0.469 267 -
all-296 -
obs--88.62 %

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