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- PDB-2lt5: Zymogen-FLG of the onconase -

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Basic information

Entry
Database: PDB / ID: 2lt5
TitleZymogen-FLG of the onconase
ComponentsProtein P-30
KeywordsHYDROLASE / ribonuclease
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
Biological speciesRana pipiens (northern leopard frog)
MethodSOLUTION NMR / energy minimization
Model detailslowest energy, model 1
AuthorsVilanova, M. / Callis, M. / Laurents, D.V. / Ribo, M. / Bruix, M. / Serrano, S.
History
DepositionMay 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein P-30


Theoretical massNumber of molelcules
Total (without water)13,2431
Polymers13,2431
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein P-30 / Onconase


Mass: 13243.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana pipiens (northern leopard frog) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P22069, 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
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D CBCANH
1413D HNCA
1513D HN(CO)CA
1613D HN(CA)CO
1713D 1H-13C NOESY
1813D 1H-15N NOESY
1913D HNCO
11012D 1H-13C HSQC
21122D 1H-13C HSQC
11212D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
125 uL buffer 10x, 200 uL H2O MQ, 2 uL DSS, 2 uL NaN3, 2.8 mM [U-100% 15N, 13C] ONC_FLG, 90% H2O/10% D2O90% H2O/10% D2O
225 uL buffer 10x, 200 uL [U-100% 2H] D2O, 2 uL DSS, 2 uL NaN3, 1.8 mM [U-100% 15N] ONC_FLG, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 %buffer 10x-11
200 %H2O MQ-21
2 %DSS-31
2 %NaN3-41
2.8 mMONC_FLG-5[U-100% 15N, 13C]1
25 %buffer 10x-62
200 %D2O-7[U-100% 2H]2
2 %DSS-82
2 %NaN3-92
1.8 mMONC_FLG-10[U-100% 15N]2
Sample conditions
Conditions-IDPressure (kPa)Temperature (K)
1ambient 308 K
2ambient 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospinprocessing
TopSpin1.3Bruker Biospinacquisition
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
TALOSTALOS +Cornilescu, Delaglio and Baxangular constraints
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: energy minimization / Software ordinal: 1 / Details: Gibbs Boltzmann minimization
NMR constraintsNOE constraints total: 2025 / NOE long range total count: 678 / NOE medium range total count: 288
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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