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- PDB-2ki3: Structural and biochemical characterization of FK506 binding doma... -

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Basic information

Entry
Database: PDB / ID: 2ki3
TitleStructural and biochemical characterization of FK506 binding domain from Plasmodium vivax
Components70 kDa peptidylprolyl isomerase, putative
KeywordsISOMERASE / Protein / TPR repeat
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
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 / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily ...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 / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
peptidylprolyl isomerase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsAlag, R. / Yoon, H.S. / Shin, J.
CitationJournal: Biomol.Nmr Assign. / Year: 2009
Title: NMR assignments of the FK506-binding domain of FK506-binding protein 35 from Plasmodium vivax
Authors: Alag, R. / Shin, J. / Yoon, H.S.
History
DepositionApr 21, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 70 kDa peptidylprolyl isomerase, putative


Theoretical massNumber of molelcules
Total (without water)13,9721
Polymers13,9721
Non-polymers00
Water0
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 energy

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Components

#1: Protein 70 kDa peptidylprolyl isomerase, putative / PvFKBD


Mass: 13971.687 Da / Num. of mol.: 1 / Fragment: residues 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Production host: Escherichia coli (E. coli) / References: UniProt: A5K8X6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CO)CA
1613D HNCO
1713D HN(CA)CO
1813D HNHA
1913D H(CCO)NH
11013D C(CO)NH
11113D 1H-15N NOESY
11223D (H)CCH-TOCSY
11323D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM [U-13C; U-15N] PvFKBD-1, 20mM sodium phosphate-2, 50mM sodium chloride-3, 1mM DTT-4, 0.01 % sodium azide-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] PvFKBD-6, 20mM sodium phosphate-7, 50mM sodium chloride-8, 1mM DTT-9, 0.01 % sodium azide-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPvFKBD-1[U-13C; U-15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMDTT-41
0.01 %sodium azide-51
0.5 mMPvFKBD-6[U-13C; U-15N]2
20 mMsodium phosphate-72
50 mMsodium chloride-82
1 mMDTT-92
0.01 %sodium azide-102
Sample conditionspH: 6.8 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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