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- PDB-5id5: Solution structure of porcine lactoferricin -

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Basic information

Entry
Database: PDB / ID: 5id5
TitleSolution structure of porcine lactoferricin
ComponentsLactoferrin
KeywordsHYDROLASE / lactoferricin / porcine
Function / homology
Function and homology information


negative regulation by host of viral process / disruption of plasma membrane integrity in another organism / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of cysteine-type endopeptidase activity / negative regulation of single-species biofilm formation in or on host organism / negative regulation of lipopolysaccharide-mediated signaling pathway / specific granule / antifungal humoral response / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity ...negative regulation by host of viral process / disruption of plasma membrane integrity in another organism / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of cysteine-type endopeptidase activity / negative regulation of single-species biofilm formation in or on host organism / negative regulation of lipopolysaccharide-mediated signaling pathway / specific granule / antifungal humoral response / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / cysteine-type endopeptidase inhibitor activity / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / positive regulation of osteoblast differentiation / monoatomic ion transport / regulation of cytokine production / protein serine/threonine kinase activator activity / ossification / innate immune response in mucosa / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / positive regulation of NF-kappaB transcription factor activity / antibacterial humoral response / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / defense response to Gram-negative bacterium / iron ion binding / serine-type endopeptidase activity / cell surface / protein-containing complex / extracellular space
Similarity search - Function
Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
Lactotransferrin / Lactotransferrin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodSOLUTION NMR / simulated annealing
AuthorsChan, M.S. / Tse, M.K. / Lo, K.C. / Sze, K.H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
RGCN.A. Hong Kong
CitationJournal: To Be Published
Title: Solution structure of porcine lactoferricin
Authors: Chan, M.S. / Tse, M.K. / Lo, K.C. / Sze, K.H.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
SupersessionApr 27, 2022ID: 5I4G
Revision 2.0Apr 27, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / pdbx_database_PDB_obs_spr / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 2.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactoferrin


Theoretical massNumber of molelcules
Total (without water)3,0411
Polymers3,0411
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2970 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Lactoferrin /


Mass: 3040.595 Da / Num. of mol.: 1 / Fragment: UNP residues 36-60 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig) / References: UniProt: Q8WMN8, UniProt: Q6YT39*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1Proton 1D
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM 1H porcine lactoferricin, trifluoroethanol/water
Details: 1mM of sample in TFE-membrane mimic environment / Label: 1H_sample / Solvent system: trifluoroethanol/water
SampleConc.: 1 mM / Component: porcine lactoferricin / Isotopic labeling: 1H
Sample conditionsIonic strength: 0 Not defined / Label: 1H_condition / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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