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- PDB-2kr7: solution structure of Helicobacter pylori SlyD -

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Basic information

Entry
Database: PDB / ID: 2kr7
Titlesolution structure of Helicobacter pylori SlyD
ComponentsFKBP-type peptidyl-prolyl cis-trans isomerase slyD
KeywordsISOMERASE / protein / Rotamase
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / metal ion binding / cytoplasm
Similarity search - Function
Thrombin, subunit H - #330 / : / 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 / Thrombin, subunit H / Roll ...Thrombin, subunit H - #330 / : / 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 / Thrombin, subunit H / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsCheng, T. / Li, H. / Xia, W. / Sze, K. / Sun, H.
CitationJournal: To be Published
Title: solution structure of Helicobacter pylori SlyD
Authors: Cheng, T. / Li, H. / Xia, W. / Sze, K. / Sun, H.
History
DepositionDec 7, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FKBP-type peptidyl-prolyl cis-trans isomerase slyD


Theoretical massNumber of molelcules
Total (without water)17,0391
Polymers17,0391
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein FKBP-type peptidyl-prolyl cis-trans isomerase slyD / PPIase / Rotamase


Mass: 17039.033 Da / Num. of mol.: 1 / Fragment: UNP residues 1-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: slyD, HP_1123 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25748, peptidylprolyl isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HN(CA)CO
1713D C(CO)NH
1813D H(CCO)NH
1913D HNCA
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
11213D HBHA(CO)NH
11313D HNHA
11413D HN(CO)CA
11513D 1H-15N NOESY
11623D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-1.5 mM [U-100% 13C; U-100% 15N] SlyD-1, 90% H2O/10% D2O90% H2O/10% D2O
21-1.5 mM [U-100% 13C; U-100% 15N] SlyD-2, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSlyD-1[U-100% 13C; U-100% 15N]1-1.51
mMSlyD-2[U-100% 13C; U-100% 15N]1-1.52
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANA, _AMBERGuntert, Mumenthaler and Wuthrichstructure solution
CYANA, _AMBERGuntert, Mumenthaler and Wuthrichrefinement
CYANA, _AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
CYANA, _AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 4

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