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- PDB-2rsx: Solution structure of IseA, an inhibitor protein of DL-endopeptid... -

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Basic information

Entry
Database: PDB / ID: 2rsx
TitleSolution structure of IseA, an inhibitor protein of DL-endopeptidases from Bacillus subtilis
ComponentsUncharacterized protein yoeB
KeywordsHYDROLASE INHIBITOR / inhibitor protein / hacksaw-like fold / autolysin inhibitor / DL-endopeptidase inhibitor
Function / homologyNuclear Transport Factor 2; Chain: A, - #420 / DL-endopeptidase inhibitor IseA / : / IseA DL-endopeptidase inhibitor / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein YoeB
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsArai, R. / Li, H. / Tochio, N. / Fukui, S. / Kobayashi, N. / Kitaura, C. / Watanabe, S. / Kigawa, T. / Sekiguchi, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Solution Structure of IseA, an Inhibitor Protein of DL-Endopeptidases from Bacillus subtilis, Reveals a Novel Fold with a Characteristic Inhibitory Loop
Authors: Arai, R. / Fukui, S. / Kobayashi, N. / Sekiguchi, J.
History
DepositionAug 9, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Data collection / Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein yoeB


Theoretical massNumber of molelcules
Total (without water)17,7281
Polymers17,7281
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein yoeB / IseA / Inhibitor protein of cell Separation Enzyme


Mass: 17728.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yoeB / Production host: E. coli CELL-FREE PROTEIN SYNTHESIS / References: UniProt: O34841

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HNCO
1613D HN(CA)CO
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HBHA(CO)NH
11013D C(CCO)NH
11113D (H)CCH-TOCSY
11213D (H)CCH-TOCSY
11313D (H)CCH-COSY
11413D 1H-15N NOESY
11513D 1H-13C NOESY

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Sample preparation

DetailsContents: 1.12 mM [U-13C; U-15N] IseA-1, 20 mM [U-2H] TRIS-2, 300 mM sodium chloride-3, 0.02 % sodium azide-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.12 mMIseA-1[U-13C; U-15N]1
20 mMTRIS-2[U-2H]1
300 mMsodium chloride-31
0.02 %sodium azide-41
Sample conditionsIonic strength: 0.3 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.17Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 3659 / NOE intraresidue total count: 852 / NOE long range total count: 1320 / NOE medium range total count: 651 / NOE sequential total count: 836
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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