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- PDB-2kw8: Solution Structure of Bacillus anthracis Sortase A (SrtA) Transpe... -

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Basic information

Entry
Database: PDB / ID: 2kw8
TitleSolution Structure of Bacillus anthracis Sortase A (SrtA) Transpeptidase
ComponentsLPXTG-site transpeptidase family protein
KeywordsPROTEIN BINDING / Sortase / SrtA / transpeptidase
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis / membrane
Similarity search - Function
Sortase A / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
LPXTG-site transpeptidase family protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 33
AuthorsWeiner, E.M. / Robson, S.A. / Marohn, M. / Clubb, R.T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The Sortase A enzyme that attaches proteins to the cell wall of Bacillus anthracis contains an unusual active site architecture.
Authors: Weiner, E.M. / Robson, S. / Marohn, M. / Clubb, R.T.
History
DepositionMar 31, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: LPXTG-site transpeptidase family protein


Theoretical massNumber of molelcules
Total (without water)17,1101
Polymers17,1101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein LPXTG-site transpeptidase family protein


Mass: 17110.387 Da / Num. of mol.: 1 / Fragment: UNP residues 80-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BA_0688, GBAA0688, GBAA_0688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81V16

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1322D 1H-13C HSQC
1423D CBCA(CO)NH
1523D C(CO)NH
1623D HNCO
1723D HNCA
1823D HN(CA)CB
1923D HBHA(CO)NH
11033D (H)CCH-TOCSY
11123D HNHA
11223D 1H-15N NOESY
11333D 1H-13C NOESY
11423D HNHB
11523D (H)CCH-COSY
11623D HCACO
11724D 15N-13C HMQC-NOESY-HSQC
11822D (HB)CB(CGCDCE)HE
11922D (HB)CB(CGCD)HD
12022D 1H-15N HSQC
12112D 1H-15N HSQC NOE with interleaved presat and no sat

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Sample preparation

Details
Solution-IDContentsSolvent system
14 mM [U-100% 15N] SrtA-1, 10 mM MES-2, 20 mM Bis-Tris-3, 93% H2O/7% D2O93% H2O/7% D2O
22.5 mM [U-100% 13C; U-100% 15N] SrtA-4, 10 mM MES-5, 20 mM Bis-Tris-6, 93% H2O/7% D2O93% H2O/7% D2O
32.5 mM [U-100% 13C; U-100% 15N] SrtA-7, 10 mM MES-8, 20 mM Bis-Tris-9, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mMSrtA-1[U-100% 15N]1
10 mMMES-21
20 mMBis-Tris-31
2.5 mMSrtA-4[U-100% 13C; U-100% 15N]2
10 mMMES-52
20 mMBis-Tris-62
2.5 mMSrtA-7[U-100% 13C; U-100% 15N]3
10 mMMES-83
20 mMBis-Tris-93
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
PIPPGarrettpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Atnos/CANDIDHerrmann, Guntert, Wuthrichchemical shift assignment
ModelFreePalmerdata analysis
ProcheckNMRLaskowski and MacArthurgeometry optimization
TALOSCornilescu, Delaglio and Baxgeometry optimization
XwinNMRBruker Biospincollection
CARAKellerchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2204 / NOE intraresidue total count: 200 / NOE long range total count: 1045 / NOE medium range total count: 384 / NOE sequential total count: 575 / Hydrogen bond constraints total count: 47 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 54 / Protein phi angle constraints total count: 114 / Protein psi angle constraints total count: 117
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 40 / Maximum lower distance constraint violation: 1.8 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 6 Å / Torsion angle constraint violation method: > 5 deg.
NMR ensemble rmsDistance rms dev: 0.05 Å / Distance rms dev error: 0.002 Å

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