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- PDB-4bf8: Fpr4 PPI domain -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4bf8
TitleFpr4 PPI domain
ComponentsFPR4
KeywordsISOMERASE / PROLINE ISOMERIZATION / FKBP / HISTONE CHAPERONE
Function / homology
Function and homology information


: / : / macrolide binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nucleosome assembly / nucleolus / nucleus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase Fpr3/Fpr4-like / Nucleoplasmin-like domain / Nucleoplasmin-like domain / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
FK506-binding protein 4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / ARIA1.2
AuthorsMonneau, Y. / Mackereth, C.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure and Activity of the Peptidyl-Prolyl Isomerase Domain from the Histone Chaperone Fpr4 Towards Histone H3 Proline Isomerization
Authors: Monneau, Y.R. / Soufari, H. / Nelson, C.J. / Mackereth, C.D.
History
DepositionMar 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3May 4, 2016Group: Atomic model / Other
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 19, 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

Downloads & links

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Assembly

Deposited unit
A: FPR4


Theoretical massNumber of molelcules
Total (without water)12,5031
Polymers12,5031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 50LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein FPR4


Mass: 12502.853 Da / Num. of mol.: 1
Fragment: PEPTIDYL PROLINE ISOMERASE (PPI) DOMAIN, RESIDUES 280-392
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL PEPTIDYL PROLYL CIS-TRANS ISOMERASE DOMAIN FROM YEAST FPR4P
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: MODIFIED PET-9D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSY / References: UniProt: Q06205, peptidylprolyl isomerase
Sequence detailsCONTAINS N-TERMINAL GLY-ALA-MET-ALA- RESIDUES FOLLOWING CLEAVAGE OF THE HIS6-TAG BY TEV PROTEAS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H
12115N-NOESY (120MS MIXING TIME)
1311H
14115N-TROSY (RDC)
1511H
16113C-NOESY (120 MS MIXING TIME)
NMR detailsText: STRUCTURE CALCULATION USED A COMBINATION OF DISTANCE RESTRAINTS (UNAMBIGUOUS AND AMBIGUOUS), DIHEDRAL ANGLE RESTRAINTS, HYDROGEN-BOND RESTRAINTS AND RESIDUAL DIPOLAR COUPLING RESTRAINTS

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Sample preparation

DetailsContents: 10% WATER/90% D2O, 100% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 292.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRPipestructure solution
Sparkystructure solution
RefinementMethod: ARIA1.2 / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 12

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