[English] 日本語
Yorodumi
- PDB-2kid: Solution Structure of the S. Aureus Sortase A-substrate Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kid
TitleSolution Structure of the S. Aureus Sortase A-substrate Complex
Components
  • (PHQ)LPA(B27) peptide
  • Sortase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SORTASE / EIGHT STRANDED BETA BARREL / TRANSPEPTIDASE / ENZYME-SUBSTRATE COMPLEX / HYDROLASE-HYDROLASE INHIBITOR complex
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
(PHQ)LPA(B27) PEPTIDE / Sortase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSuree, N. / Liew, C.K. / Villareal, V.A. / Thieu, W. / Fadeev, E.A. / Clemens, J.J. / Jung, M.E. / Clubb, R.T.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The structure of the Staphylococcus aureus sortase-substrate complex reveals how the universally conserved LPXTG sorting signal is recognized.
Authors: Suree, N. / Liew, C.K. / Villareal, V.A. / Thieu, W. / Fadeev, E.A. / Clemens, J.J. / Jung, M.E. / Clubb, R.T.
History
DepositionMay 1, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Feb 26, 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_nmr_spectrometer / struct_conn / 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_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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sortase
C: (PHQ)LPA(B27) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3483
Polymers17,3082
Non-polymers401
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 / 400structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

-
Components

#1: Protein Sortase


Mass: 16753.000 Da / Num. of mol.: 1 / Fragment: Residues 62-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: srtA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9S446
#2: Protein/peptide (PHQ)LPA(B27) peptide


Type: Peptide-like / Class: Inhibitor / Mass: 555.129 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthesized substrate that mimics the LPXTG motif (native) substrate
References: (PHQ)LPA(B27) PEPTIDE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-15N TOCSY
1533D 1H-13C NOESY
1633D CBCA(CO)NH
1733D C(CO)NH
1833D HNCO
1933D HN(CA)CB
11033D HBHA(CO)NH
11133D (H)CCH-TOCSY
11233D HNHA
11333D HNHB
11433D (H)CCH-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Sortase A, 1 mM Cbz-LPAT*, 50 mM TRIS, 100 mM sodium chloride, 20 mM Calcium Chloride, 0.01 % sodium azide, 93 % H2O, 7 % [U-100% 2H] D2O, 93% H2O, 7% D2O93% H2O/7% D2O
21 mM [U-100% 15N] Sortase A, 1 mM Cbz-LPAT*, 50 mM TRIS, 100 mM sodium chloride, 20 mM Calcium Chloride, 0.01 % sodium azide, 93 % H2O, 7 % [U-100% 2H] D2O, 93% H2O, 7% D2O93% H2O/7% D2O
31 mM [U-100% 13C; U-100% 15N] Sortase A, 1 mM Cbz-LPAT*, 50 mM TRIS, 100 mM sodium chloride, 20 mM Calcium Chloride, 0.01 % sodium azide, 100 % [U-100% 2H] D2O, 93% H2O, 7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSortase A-1[U-100% 13C; U-100% 15N]1
1 mMCbz-LPAT*-21
50 mMTRIS-31
100 mMsodium chloride-41
20 mMCalcium Chloride-51
0.01 %sodium azide-61
93 %H2O-71
7 %D2O-8[U-100% 2H]1
1 mMSortase A-9[U-100% 15N]2
1 mMCbz-LPAT*-102
50 mMTRIS-112
100 mMsodium chloride-122
20 mMCalcium Chloride-132
0.01 %sodium azide-142
93 %H2O-152
7 %D2O-16[U-100% 2H]2
1 mMSortase A-17[U-100% 13C; U-100% 15N]3
1 mMCbz-LPAT*-183
50 mMTRIS-193
100 mMsodium chloride-203
20 mMCalcium Chloride-213
0.01 %sodium azide-223
100 %D2O-23[U-100% 2H]3
Sample conditionsIonic strength: 0.15 / pH: 6.0 / Pressure: AMBIENT / Temperature: 302 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER AVANCEBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHBrunger A. T. et.al.refinement
PIPPGarrettpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
ProcheckNMRLaskowski and MacArthurrefinement
MOLMOLKoradi, Billeter and Wuthrichstructure solution
SparkyGoddardpeak picking
Atnos/CandidHerrmann, Guntert and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: SOFTWARE USED: PIPP, NMRPIPE, ATNOS/CANDID, REFINEMENT: Residual Dipolar Couplings (RDC)
NMR constraintsNOE constraints total: 2454 / Protein chi angle constraints total count: 127
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 400 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more