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- PDB-2ke0: Solution structure of peptidyl-prolyl cis-trans isomerase from Bu... -

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Basic information

Entry
Database: PDB / ID: 2ke0
TitleSolution structure of peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / peptidyl-prolyl cis-trans isomerase / BupsA.00130.a / FK506 binding protein FKBP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / metal ion binding
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest target function, model 1
AuthorsZheng, S. / Leeper, T. / Napuli, A. / Nakazawa, S.H. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Biochem.J. / Year: 2011
Title: The structure of a Burkholderia pseudomallei immunophilin-inhibitor complex reveals new approaches to antimicrobial development.
Authors: Norville, I.H. / O'Shea, K. / Sarkar-Tyson, M. / Zheng, S. / Titball, R.W. / Varani, G. / Harmer, N.J.
History
DepositionJan 21, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)12,2401
Polymers12,2401
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)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest target function

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 12239.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: fbp, BPSS1823 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLys / References: UniProt: Q63J95, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: peptidyl-prolyl cis-trans isomerase
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D HNCA
1413D HN(CO)CA
1513D (H)CCH-TOCSY
1613D 1H-13C NOESY
1722D 1H-15N HSQC
1823D 1H-15N NOESY
1932D 1H-15N HSQC
11032D 1H-1H TOCSY
11132D 1H-1H NOESY
11223D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] potassium phosphate-1, 95% H2O/5% D2O95% H2O/5% D2O
20.6 mM [U-100% 15N] potassium phosphate-2, 95% H2O/5% D2O95% H2O/5% D2O
30.6 mM [U-100% 15N] potassium phosphate-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMpotassium phosphate-1[U-100% 13C; U-100% 15N]1
0.6 mMpotassium phosphate-2[U-100% 15N]2
0.6 mMpotassium phosphate-3[U-100% 15N]3
Sample conditionspH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AMXBrukerAMX7502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.structure solution
CYANA2.1P.GUNTERT ET AL.refinement
CcpNmr Analysis1CCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1792 / NOE long range total count: 799 / NOE medium range total count: 216 / NOE sequential total count: 777
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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