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- PDB-6wbu: Putative Peptidyl Prolyl cis-trans Isomerase FKBP12 from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 6wbu
TitlePutative Peptidyl Prolyl cis-trans Isomerase FKBP12 from Mycobacterium tuberculosis
ComponentsFKBP12 from Mycobacterium tuberculosis
KeywordsCYTOSOLIC PROTEIN / Isomerase / FKBP / Chaperone
Function / homologyChitinase A; domain 3 - #40 / Chitinase A; domain 3 / Roll / Alpha Beta
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAndrade, G.C. / Silva, L.F.C. / Almeida, F.C.L. / AnoBom, C.D.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)309564/2017-4 Brazil
CitationJournal: To Be Published
Title: Structure and Biochemical Characterization of a Putative Peptidyl Prolyl cis-trans Isomerase FKBP12 from Mycobacterium tuberculosis
Authors: Andrade, G.C. / Silva, L.F.C. / Oliveira, D.M.P. / Pires, J.R.M. / Almeida, F.C.L. / Anobom, C.D.
History
DepositionMar 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FKBP12 from Mycobacterium tuberculosis


Theoretical massNumber of molelcules
Total (without water)13,4571
Polymers13,4571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein FKBP12 from Mycobacterium tuberculosis


Mass: 13457.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: 401416 / Gene: fkbP_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: 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
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
181isotropic13D HNCA
171isotropic13D HN(CA)CB
191isotropic13D HN(CA)CO
161isotropic13D HBHA(CO)NH
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY aliphatic
1131isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1.2 mM [U-13C; U-15N] FKBP12 from Mycobacterium tuberculosis, 90% H2O/10% D2O
Label: 15N_13C_MtFKBP / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMFKBP12 from Mycobacterium tuberculosis[U-13C; U-15N]1
2 mMPMSFnatural abundance2
5 mMEDTAnatural abundance3
5 mMsodium azidenatural abundance4
150 mMsodium chloridenatural abundance5
50 mMsodium phosphatenatural abundance6
Sample conditionsIonic strength: 0.22 M / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE IIIBrukerAVANCE III9002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
TopSpin3.1Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA2.2Linge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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