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- PDB-5zr0: Solution structure of peptidyl-prolyl cis/trans isomerase domain ... -

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Basic information

Entry
Database: PDB / ID: 5zr0
TitleSolution structure of peptidyl-prolyl cis/trans isomerase domain of Trigger Factor in complex with MBP
ComponentsMaltose-binding periplasmic protein,Trigger factor
KeywordsCHAPERONE / Molecular Chaperone / Peptidyl-prolyl isomerases
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / protein transport / outer membrane-bounded periplasmic space / periplasmic space / cell cycle / cell division / DNA damage response / membrane / cytoplasm
Similarity search - Function
Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. ...Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Trigger factor / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsKawagoe, S. / Nakagawa, H. / Kumeta, H. / Ishimori, K. / Saio, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyPRESTO Japan
Japan Society for the Promotion of ScienceKAKENHI (17H05657) Japan
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural insight into prolinecis/transisomerization of unfolded proteins catalyzed by the trigger factor chaperone.
Authors: Kawagoe, S. / Nakagawa, H. / Kumeta, H. / Ishimori, K. / Saio, T.
History
DepositionApr 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.2May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Trigger factor


Theoretical massNumber of molelcules
Total (without water)15,1351
Polymers15,1351
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8980 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Maltose-binding periplasmic protein,Trigger factor / MBP / MMBP / Maltodextrin-binding protein / TF / PPIase


Mass: 15134.620 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: malE, b4034, JW3994, tig, BWG_0318 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEX9, UniProt: C4ZTJ3, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic23D HNCA
151isotropic23D HN(CA)CB
161isotropic23D HNCO
171isotropic23D HN(CO)CA
181isotropic23D CBCA(CO)NH
191isotropic23D HNCAHA
1101isotropic23D HBHA(CO)NH
1111isotropic13D (H)CCH-TOCSY
1121isotropic13D (H)CCH-TOCSY
1131isotropic22D (HB)CB(CGCD)HD
1141isotropic22D (HB)CB(CGCDCE)HE
1151isotropic13D 1H-15N NOESY
1161isotropic13D 1H-13C NOESY aliphatic
1171isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] MBP238-266-PPD fusion, 90% H2O/10% D2O
Label: 13C15N MBP-PPD / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: MBP238-266-PPD fusion / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 100 mM / Label: condition-1 / pH: 7.0 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY8001
Varian UNITYVarianUNITY6002

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Processing

NMR software
NameDeveloperClassification
OliviaMasashi Yokochidata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
OliviaMasashi Yokochichemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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