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- PDB-2k23: Solution Structure Analysis of the rLcn2 -

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Basic information

Entry
Database: PDB / ID: 2k23
TitleSolution Structure Analysis of the rLcn2
ComponentsLipocalin 2
KeywordsTRANSPORT PROTEIN / beta barrel
Function / homology
Function and homology information


Metal sequestration by antimicrobial proteins / Iron uptake and transport / cytoplasmic vesicle lumen / positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / siderophore transport / response to kainic acid ...Metal sequestration by antimicrobial proteins / Iron uptake and transport / cytoplasmic vesicle lumen / positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / siderophore transport / response to kainic acid / response to mycotoxin / response to blue light / cellular response to increased oxygen levels / response to fructose / cellular response to X-ray / short-term memory / cellular response to interleukin-6 / iron ion sequestering activity / enterobactin binding / response to herbicide / Neutrophil degranulation / response to iron(II) ion / positive regulation of reactive oxygen species biosynthetic process / cellular response to interleukin-1 / long-term memory / cellular response to nutrient levels / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of endothelial cell migration / acute-phase response / response to bacterium / response to nutrient levels / cellular response to nerve growth factor stimulus / response to toxic substance / response to virus / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / cellular response to amyloid-beta / cellular response to tumor necrosis factor / positive regulation of neuron apoptotic process / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / response to oxidative stress / protease binding / response to lipopolysaccharide / cellular response to hypoxia / defense response to bacterium / positive regulation of apoptotic process / iron ion binding / response to xenobiotic stimulus / innate immune response / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Neutrophil gelatinase-associated lipocalin / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZhang, F. / Lin, D.H.
CitationJournal: To be Published
Title: NMR solution structure of rat lipocalin 2
Authors: Zhang, F. / Lin, D.H.
History
DepositionMar 21, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipocalin 2


Theoretical massNumber of molelcules
Total (without water)20,5141
Polymers20,5141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lipocalin 2


Mass: 20513.975 Da / Num. of mol.: 1 / Fragment: UNP residues 21-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lcn2 / Plasmid: pet22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HZF1, UniProt: P30152*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.8mM [U-99% 13C; U-99% 15N] sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: sodium phosphate / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.15 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue, Nilgesstructure solution
ARIALinge, O'Donoghue, Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 15

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