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- PDB-3zua: A C39-like domain -

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Basic information

Entry
Database: PDB / ID: 3zua
TitleA C39-like domain
ComponentsALPHA-HEMOLYSIN TRANSLOCATION ATP-BINDING PROTEIN HLYB
KeywordsHYDROLASE / C39 PEPTIDASE-LIKE DOMAIN / ABC TRANSPORTER / HAEMOLYSIN / HETERONUCLEAR NMR
Function / homology
Function and homology information


type I protein secretion system complex / protein secretion by the type I secretion system / ATPase-coupled transmembrane transporter activity / peptidase activity / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Cysteine proteinases / Type 1 protein exporter / Cathepsin B; Chain A / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain ...ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Cysteine proteinases / Type 1 protein exporter / Cathepsin B; Chain A / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Alpha-hemolysin translocation ATP-binding protein HlyB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / ARIA
AuthorsLecher, J. / Schwarz, C.K.W. / Stoldt, M. / Smits, S.S.H. / Willbold, D. / Schmitt, L.
CitationJournal: Structure / Year: 2012
Title: An Rtx Transporter Tethers its Unfolded Substrate During Secretion Via a Unique N-Terminal Domain.
Authors: Lecher, J. / Schwarz, C.K.W. / Stoldt, M. / Smits, S.S.H. / Willbold, D. / Schmitt, L.
History
DepositionJul 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Oct 31, 2012Group: Database references
Revision 1.4Nov 7, 2012Group: Structure summary
Revision 2.0May 15, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-HEMOLYSIN TRANSLOCATION ATP-BINDING PROTEIN HLYB


Theoretical massNumber of molelcules
Total (without water)16,1061
Polymers16,1061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100MINIMAL ENERGY
RepresentativeModel #1

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Components

#1: Protein ALPHA-HEMOLYSIN TRANSLOCATION ATP-BINDING PROTEIN HLYB / CLD


Mass: 16106.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q47258, papain
Sequence detailsAS A RESULT OF CLONING STRATEGY AND PROTEASE DIGESTION, THE SEQUENCE N-TERMINAL TO THE WT POSITION ...AS A RESULT OF CLONING STRATEGY AND PROTEASE DIGESTION, THE SEQUENCE N-TERMINAL TO THE WT POSITION 2 IS GAMANS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY (ALIPHATIC
121AROMATIC
131AMID)
NMR detailsText: THE STRUCTURE WAS DETERMINED BY NOE DERIVED DISTANCE RESTRAINTS FROM (1H-1H-13C)-NOESY-HSQC ALIPHATIC & AROMATIC AND (1H-15N-1H)-HSQC-NOESY USING CHEMICAL SHIFT ASSIGNMENTS DEPOSITED IN BMRB ENTRY 17403.

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Sample preparation

DetailsContents: 93% H2O/7% D2O
Sample conditionsIonic strength: 0.2 / pH: 6 / Pressure: 1.0 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS 1.21 WITH ARIA PATCHESPATCHESBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
DANGLE1.1structure solution
VnmrJ2.3Astructure solution
ARIA2.3.1structure solution
Azara2.8structure solution
CcpNmr Analysis2.1structure solution
NMRPipe5.4.2010.250.17.50structure solution
TALOS+13.41structure solution
RefinementMethod: ARIA / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: MINIMAL ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 10

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