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- PDB-2k11: Solution structure of human pancreatic ribonuclease -

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Basic information

Entry
Database: PDB / ID: 2k11
TitleSolution structure of human pancreatic ribonuclease
ComponentsPancreatic RibonucleasePancreatic ribonuclease family
KeywordsHYDROLASE / Endonuclease / Glycoprotein / Nuclease / Secreted
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / Late endosomal microautophagy / Chaperone Mediated Autophagy / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular exosome
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKover, K.E. / Bruix, M. / Santoro, J. / Batta, G. / Laurents, D.V. / Rico, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition.
Authors: Kover, K.E. / Bruix, M. / Santoro, J. / Batta, G. / Laurents, D.V. / Rico, M.
History
DepositionFeb 20, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pancreatic Ribonuclease


Theoretical massNumber of molelcules
Total (without water)14,4961
Polymers14,4961
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Pancreatic Ribonuclease / Pancreatic ribonuclease family / RNase 1 / RNase A / RNase UpI-1 / RIB-1 / HP-RNase


Mass: 14496.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE1, RIB1, RNS1 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P07998, EC: 3.1.27.5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-1H COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY
1733D 1H-15N TOCSY
1833D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM Human pancreatic ribonuclease, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM Human pancreatic ribonuclease, 100% D2O100% D2O
31.2 mM [U-15N] Human pancreatic ribonuclease, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMHuman pancreatic ribonuclease1
1.2 mMHuman pancreatic ribonuclease2
1.2 mMHuman pancreatic ribonuclease[U-15N]3
Sample conditionspH: 4.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
XEASYBartels, C. et al.chemical shift assignment
CYANAGuntert, P. et al.refinement
RefinementMethod: simulated annealing / 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: 20

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