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- PDB-2mly: NMR structure of E. coli Trigger Factor in complex with unfolded ... -

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Basic information

Entry
Database: PDB / ID: 2mly
TitleNMR structure of E. coli Trigger Factor in complex with unfolded PhoA1-150
Components
  • Alkaline phosphatase
  • Trigger factor
KeywordsCHAPERONE / molecular chaperone / unfolded protein
Function / homology
Function and homology information


Trigger factor, domain 2 / Trigger factor, C-terminal domain / Trigger factor ribosome-binding domain / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsSaio, T. / Guan, X. / Rossi, P. / Economou, A. / Kalodimos, C.G.
CitationJournal: Science / Year: 2014
Title: Structural basis for protein antiaggregation activity of the trigger factor chaperone.
Authors: Saio, T. / Guan, X. / Rossi, P. / Economou, A. / Kalodimos, C.G.
History
DepositionMar 5, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trigger factor
B: Alkaline phosphatase


Theoretical massNumber of molelcules
Total (without water)65,6022
Polymers65,6022
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)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Trigger factor / TF / PPIase


Mass: 49696.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tig, BN896_0318 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U6N325, peptidylprolyl isomerase
#2: Protein Alkaline phosphatase


Mass: 15905.933 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phoA, BN896_0267 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U6N3P1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-13C NOESY
1413D 1H-15N NOESY
1513D HN(CA)CB
1613D 1H-13C HMQC-NOESY HMQC
1712D 1H-13C HMQC
1813D (H)CCH-TOCSY
1913D H(CCO)NH

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] Alkaline phosphatase, 0.5 mM [U-100% 13C; U-100% 15N] Trigger Factor, 100 mM potassium chloride, 3 mM BME, 20 mM potassium phosphate, 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAlkaline phosphatase[U-100% 13C; U-100% 15N]1
0.5 mMTrigger Factor[U-100% 13C; U-100% 15N]1
100 mMpotassium chloride-31
3 mMBME-41
20 mMpotassium phosphate-51
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE6004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
Olivia1.16Olivia, Yokochi Masashichemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin3.1Bruker Biospincollection
VnmrJVariancollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSNShen and Baxgeometry optimization
PSVS1.5Bhattacharya and Montelionevalidation
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1896 / NOE intraresidue total count: 375 / NOE long range total count: 781 / NOE medium range total count: 257 / NOE sequential total count: 483
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10
NMR ensemble rmsDistance rms dev: 0.04 Å

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