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- PDB-2rui: Solution Structure of the Bacillus anthracis Sortase A-substrate ... -

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Basic information

Entry
Database: PDB / ID: 2rui
TitleSolution Structure of the Bacillus anthracis Sortase A-substrate Complex
Components
  • Boc-LPAT*
  • LPXTG-site transpeptidase family protein
KeywordsHYDROLASE/HYDROLASE SUBSTRATE / Sortase / SrtA / Transpeptidase / HYDROLASE-HYDROLASE SUBSTRATE complex
Function / homology
Function and homology information


cysteine-type peptidase activity / membrane => GO:0016020 / 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
(BOC)LPA(B27) PEPTIDE / Class A sortase / LPXTG-site transpeptidase family protein
Similarity search - Component
Biological speciesBacillus anthracis str. Sterne (bacteria)
synthetic (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsChan, A.H. / Yi, S. / Jung, M.E. / Clubb, R.T.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure of the Bacillus anthracis Sortase A Enzyme Bound to Its Sorting Signal: A FLEXIBLE AMINO-TERMINAL APPENDAGE MODULATES SUBSTRATE ACCESS.
Authors: Chan, A.H. / Yi, S.W. / Terwilliger, A.L. / Maresso, A.W. / Jung, M.E. / Clubb, R.T.
History
DepositionJun 22, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_nmr_software ...citation / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPXTG-site transpeptidase family protein
B: Boc-LPAT*


Theoretical massNumber of molelcules
Total (without water)17,6132
Polymers17,6132
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 / 200structures with the lowest energy
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 57-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. Sterne (bacteria)
Gene: BAS0654, srtA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6I399, UniProt: Q81V16*PLUS
#2: Protein/peptide Boc-LPAT*


Type: Peptide-like / Class: Inhibitor / Mass: 502.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others) / References: (BOC)LPA(B27) PEPTIDE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D C(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1823D (H)CCH-TOCSY
1913D HNHA
11013D 1H-15N NOESY
11123D 1H-13C NOESY
11213D HNHB
11323D (H)CCH-COSY
11413D HCACO
11513D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
12.6 mM [U-100% 13C; U-100% 15N] BaSrtA-1, 2.6 mM Boc-LPAT*-2, 50 mM sodium phosphate-3, 0.01 % sodium azide-4, 93% H2O/7% D2O93% H2O/7% D2O
22.6 mM [U-100% 13C; U-100% 15N] BaSrtA-5, 2.6 mM Boc-LPAT*-6, 50 mM sodium phosphate-7, 0.01 % sodium azide-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.6 mMBaSrtA-1[U-100% 13C; U-100% 15N]1
2.6 mMBoc-LPAT*-21
50 mMsodium phosphate-31
0.01 %sodium azide-41
2.6 mMBaSrtA-5[U-100% 13C; U-100% 15N]2
2.6 mMBoc-LPAT*-62
50 mMsodium phosphate-72
0.01 %sodium azide-82
Sample conditionsIonic strength: 50 / pH: 6.0 / 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
NameVersionDeveloperClassification
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorerefinement
ModelFreePalmerdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
XwinNMRBruker Biospincollection
XwinNMRBruker Biospindata analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
UNIO10Herrmann, Guntert and Wuthrichpeak picking
UNIO10Herrmann, Guntert and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1861 / NOE intraresidue total count: 368 / NOE long range total count: 808 / NOE medium range total count: 235 / NOE sequential total count: 449 / Hydrogen bond constraints total count: 47 / Protein chi angle constraints total count: 24 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 150 / Protein psi angle constraints total count: 144
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.031 Å / Distance rms dev error: 0.002 Å

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