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- PDB-2jzv: Solution structure of S. aureus PrsA-PPIase -

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Basic information

Entry
Database: PDB / ID: 2jzv
TitleSolution structure of S. aureus PrsA-PPIase
ComponentsFoldase protein prsA
KeywordsISOMERASE / PPIase / parvulin / foldase / Staphylococcus aureus / proline isomerase / Lipoprotein / Membrane / Palmitate / Rotamase
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / plasma membrane
Similarity search - Function
Foldase protein PrsA / Trigger factor/SurA domain superfamily / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Foldase protein PrsA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsSeppala, R. / Tossavainen, H. / Heikkinen, S. / Koskela, H. / Kontinen, V. / Permi, P.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA - Implications for the catalytic mechanism of parvulins.
Authors: Heikkinen, O. / Seppala, R. / Tossavainen, H. / Heikkinen, S. / Koskela, H. / Permi, P. / Kilpelainen, I.
History
DepositionJan 21, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: 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_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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
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: Foldase protein prsA


Theoretical massNumber of molelcules
Total (without water)12,2161
Polymers12,2161
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)25 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Foldase protein prsA


Mass: 12215.917 Da / Num. of mol.: 1 / Fragment: UNP residues 140-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: ATCC 292B / Gene: prsA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P60747, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D C(CO)NH
1523D HNCO
1623D HN(CA)CB
1723D HN(CO)CA
1823D H(CCO)NH
1923D (H)CCH-TOCSY
11023D (H)CCH-COSY
11123D 1H-15N NOESY
11223D 1H-13C NOESY
11323D iHNCA
11423D 1H-13C NOESY (AROM)
1152(H )C (C C )H
1162(H )C (C C C )H
1172J(CN) intensity MODULATED constant time 13C-HSQC
11813D R1 resolved 1H-15N-HSQC
11913D R2 resolved 1H-15N-HSQC
1201exchange rate resolved 1H-15N-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-15N] PrsA-PPIase, 20 mM Bis-TRIS, 1 mM sodium azide, 1 mM EDTA, 92% H2O/8% D2O92% H2O/8% D2O
21 mM [U-15N] PrsA-PPIase, 20 mM Bis-TRIS, 1 mM sodium azide, 1 mM EDTA, 92% H2O/8% D2O92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMPrsA-PPIase[U-15N]1
20 mMBis-TRIS1
1 mMsodium azide1
1 mMEDTA1
1 mMPrsA-PPIase[U-15N]2
20 mMBis-TRIS2
1 mMsodium azide2
1 mMEDTA2
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003
Bruker DRXBrukerDRX5004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
VNMR6.1CVarianprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddarddata analysis
Sparky3.11Goddardpeak picking
TALOS2003.027.13.05Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
ProcheckNMRLaskowski and MacArthurquality control
What_checkVriendquality control
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Structures were refined with molecular dynamics using Born implicit solvent model in AMBER 8.0
NMR constraintsNOE constraints total: 2161
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 25 / Maximum upper distance constraint violation: 0.16 Å

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