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- PDB-4eyc: Crystal structure of the cathelin-like domain of human cathelicid... -

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Basic information

Entry
Database: PDB / ID: 4eyc
TitleCrystal structure of the cathelin-like domain of human cathelicidin LL-37 (hCLD)
ComponentsCathelicidin antimicrobial peptide
KeywordsUNKNOWN FUNCTION / cathelin-like domain / pro-domain of human cathelicidin LL-37 / cystatin-like fold / 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 / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, ...Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Cathelicidin antimicrobial peptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPazgier, M. / Pozharski, E. / Toth, E. / Lu, W.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and Functional Analysis of the Pro-Domain of Human Cathelicidin, LL-37.
Authors: Pazgier, M. / Ericksen, B. / Ling, M. / Toth, E. / Shi, J. / Li, X. / Galliher-Beckley, A. / Lan, L. / Zou, G. / Zhan, C. / Yuan, W. / Pozharski, E. / Lu, W.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)23,9412
Polymers23,9412
Non-polymers00
Water2,396133
1
A: Cathelicidin antimicrobial peptide


Theoretical massNumber of molelcules
Total (without water)11,9701
Polymers11,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cathelicidin antimicrobial peptide


Theoretical massNumber of molelcules
Total (without water)11,9701
Polymers11,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.146, 57.987, 39.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cathelicidin antimicrobial peptide / 18 kDa cationic antimicrobial protein / CAP-18 / hCAP-18 / Antibacterial protein FALL-39 / FALL-39 ...18 kDa cationic antimicrobial protein / CAP-18 / hCAP-18 / Antibacterial protein FALL-39 / FALL-39 peptide antibiotic / Antibacterial protein LL-37


Mass: 11970.497 Da / Num. of mol.: 2
Fragment: pro-domain of human cathelicidin LL-37, UNP residues 31-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMP, CAP18, FALL39, HSD26 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49913
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 m SODIUM HEPES, 0.2 m SODIUM CITRATE, 20% ISOPROPANOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 16840 / Num. obs: 16740 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.93→2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 6.1 / Rsym value: 0.301 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PFP

1pfp


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.181 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 815 5 %RANDOM
Rwork0.1912 ---
obs0.1938 16266 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.7 Å2 / Biso mean: 39.0598 Å2 / Biso min: 22.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--2.09 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 0 133 1705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021655
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.9912234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2125208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20824.54577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59215307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5861515
X-RAY DIFFRACTIONr_chiral_restr0.1270.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211246
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 37 -
Rwork0.228 767 -
all-804 -
obs--69.61 %

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