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- PDB-2kf4: Barnase high pressure structure -

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Basic information

Entry
Database: PDB / ID: 2kf4
TitleBarnase high pressure structure
ComponentsRibonuclease
KeywordsHYDROLASE / barnase / ribonuclease / pressure / Endonuclease / Nuclease / Secreted / SIGNALING PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region
Similarity search - Function
: / Barnase / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsall equally good, model 1
AuthorsWilliamson, M.P. / Wilton, D.J.
CitationJournal: Biophys.J. / Year: 2009
Title: Pressure-dependent structure changes in barnase on ligand binding reveal intermediate rate fluctuations.
Authors: Wilton, D.J. / Kitahara, R. / Akasaka, K. / Pandya, M.J. / Williamson, M.P.
History
DepositionFeb 11, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease


Theoretical massNumber of molelcules
Total (without water)12,3321
Polymers12,3321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 5010 randomly selected
RepresentativeModel #1all equally good

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Components

#1: Protein Ribonuclease / Barnase / RNase Ba


Mass: 12331.651 Da / Num. of mol.: 1 / Mutation: H102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: For comparison to low pressure structure (pdb 2kf3)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC

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Sample preparation

DetailsContents: 1.1 mM [U-100% 13C; U-100% 15N] barnase, 30 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMbarnase[U-100% 13C; U-100% 15N]1
30 mMsodium phosphate1
Sample conditionspH: 6.7 / Pressure: 200 0 / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORBrungerstructure solution
X-PLORBrungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Shifts restrained to starting values plus changes to high pressure
NMR representativeSelection criteria: all equally good
NMR ensembleConformer selection criteria: 10 randomly selected / Conformers calculated total number: 50 / Conformers submitted total number: 10

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