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- PDB-1ija: Structure of Sortase -

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Basic information

Entry
Database: PDB / ID: 1ija
TitleStructure of Sortase
ComponentsSortase
KeywordsPROTEIN BINDING / Eight stranded Beta Barrel / Transpeptidase
Function / homology
Function and homology information


calcium-dependent cysteine-type endopeptidase activity / ion binding / peptide binding / manganese ion binding / calcium ion binding / magnesium ion binding / proteolysis
Similarity search - Function
Sortase A / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsIlangovan, U. / Ton-That, H. / Iwahara, J. / Schneewind, O. / Clubb, R.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of sortase, the transpeptidase that anchors proteins to the cell wall of Staphylococcus aureus.
Authors: Ilangovan, U. / Ton-That, H. / Iwahara, J. / Schneewind, O. / Clubb, R.T.
History
DepositionApr 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortase


Theoretical massNumber of molelcules
Total (without water)16,7531
Polymers16,7531
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 150structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Sortase /


Mass: 16753.000 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (RESIDUES 60-206)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: OS2 / Plasmid: pET9a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9S446

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N edited NOESY
1214D 15N/13C edited NOESY
1313D 13C edited NOESY
1414D 13C/13C edited NOESY
NMR detailsText: This structure was determined using triple resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 2.5 mM Sortase 15N,13C; 50 mM Tris (pH 6.2); 20 mM CaCl2; 100 mM NaCl; 3 mM DTT; 93 % H2O; 7 % D2O
Solvent system: 93% H2O/7% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.2 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe1.7Delaglio, F.processing
NMRView4.1.3Johnson, B.A. & Blevins, R.A.data analysis
X-PLOR3.843Brunger, T.A.structure solution
X-PLOR3.843Brunger, T.A.refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 2105 experimental restraints, 1852 NOE-derived distance restraints, 195 dihedral angle restraints, 58 Coupling constant restaints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
Conformers calculated total number: 150 / Conformers submitted total number: 25

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