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- PDB-2hky: NMR solution structure of human RNase 7 -

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Basic information

Entry
Database: PDB / ID: 2hky
TitleNMR solution structure of human RNase 7
ComponentsRibonuclease 7
KeywordsHYDROLASE / RNase / antimicrobial activity
Function / homology
Function and homology information


disruption of plasma membrane integrity in another organism / peptidoglycan binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / antimicrobial humoral response / Antimicrobial peptides / defense response to fungus / RNA nuclease activity / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response ...disruption of plasma membrane integrity in another organism / peptidoglycan binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / antimicrobial humoral response / Antimicrobial peptides / defense response to fungus / RNA nuclease activity / lipopolysaccharide binding / 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 / extracellular space / extracellular region / cytoplasm
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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
AuthorsHuang, Y.-C. / Chen, C. / Lou, Y.-C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The flexible and clustered lysine residues of human ribonuclease 7 are critical for membrane permeability and antimicrobial activity.
Authors: Huang, Y.C. / Lin, Y.M. / Chang, T.W. / Wu, S.J. / Lee, Y.S. / Chang, M.D. / Chen, C. / Wu, S.H. / Liao, Y.D.
History
DepositionJul 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _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: Ribonuclease 7


Theoretical massNumber of molelcules
Total (without water)14,7141
Polymers14,7141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribonuclease 7 / / RNase 7 / Skin-derived antimicrobial protein 2 / SAP-2


Mass: 14714.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE7 / Plasmid: pET 22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9H1E1, 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
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 0.6mM human RNase 7 with uniform labeling with 13C, 15N; 20mM phosphate, 1000mM NaCl buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 3.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
X-PLOR2.9.4aSchwieters, C. D.structure solution
AURELIA3.1.6Brukerdata analysis
NMRPipe5Delaglio, F.processing
XwinNMR3.5Brukerprocessing
X-PLOR2.9.4aSchwieters, C. D.refinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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