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- PDB-2kb5: Solution NMR Structure of Eosinophil Cationic Protein/RNase 3 -

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Basic information

Entry
Database: PDB / ID: 2kb5
TitleSolution NMR Structure of Eosinophil Cationic Protein/RNase 3
ComponentsEosinophil cationic protein
KeywordsHYDROLASE / ribonuclease / Antibiotic / Antimicrobial / Endonuclease / Glycoprotein / Polymorphism
Function / homology
Function and homology information


induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide ...induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / endonuclease activity / defense response to Gram-negative bacterium / nucleic acid binding / defense response to Gram-positive bacterium / innate immune response / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Eosinophil cationic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRico, M. / Bruix, M. / Laurents, D.V. / Santoro, J. / Jimenez, M. / Boix, E. / Moussaoui, M. / Nogues, M.
CitationJournal: Biopolymers / Year: 2009
Title: The (1)H, (13)C, (15)N resonance assignment, solution structure, and residue level stability of eosinophil cationic protein/RNase 3 determined by NMR spectroscopy
Authors: Laurents, D.V. / Bruix, M. / Jimenez, M.A. / Santoro, J. / Boix, E. / Moussaoui, M. / Nogues, M.V. / Rico, M.
History
DepositionNov 20, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eosinophil cationic protein


Theoretical massNumber of molelcules
Total (without water)15,5991
Polymers15,5991
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Eosinophil cationic protein / / ECP / Ribonuclease 3 / RNase 3


Mass: 15598.876 Da / Num. of mol.: 1 / Mutation: T97R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE3, ECP, RNS3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: P12724, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H COSY
1222D 1H-1H NOESY
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1512D 1H-15N HSQC
1613D 1H-15N TOCSY
1713D 1H-15N NOESY
1833D HNCA
1933D HNCO
11023D HN(CO)CA
11133D HN(CA)CB
11233D CBCA(CO)NH
11333D (H)CCH-TOCSY
11433D HCCC-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-95% 15N] ECP, 50 mM potassium phosphate, traces DSS, <1 mM potassium chloride, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-95% 15N] ECP, traces DSS, 50 mM potassium phosphate, <10 mM sodium chloride, 100% D2O100% D2O
31 mM [U-95% 13C; U-95% 15N] ECP, traces DSS, 50 mM potassium phosphate, <10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingSolution-ID
1 mMECP[U-95% 15N]1
50 mMpotassium phosphate1
%DSS1
1 mMpotassium chloride1
1 mMECP[U-95% 15N]2
%DSS2
50 mMpotassium phosphate2
10 mMsodium chloride2
1 mMECP[U-95% 13C; U-95% 15N]3
%DSS3
50 mMpotassium phosphate3
10 mMsodium chloride3
Sample conditionsIonic strength: <0.1 / pH: 4.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.processing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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