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- PDB-1fjd: HUMAN PARVULIN-LIKE PEPTIDYL PROLYL CIS/TRANS ISOMERASE, HPAR14 -

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Basic information

Entry
Database: PDB / ID: 1fjd
TitleHUMAN PARVULIN-LIKE PEPTIDYL PROLYL CIS/TRANS ISOMERASE, HPAR14
ComponentsPEPTIDYL PROLYL CIS/TRANS ISOMERASE (PPIASE)
KeywordsISOMERASE / Parvulin / Peptidyl prolyl cis/trans isomerase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


preribosome / bent DNA binding / localization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spindle / rRNA processing / chromosome / double-stranded DNA binding / mitochondrial matrix ...preribosome / bent DNA binding / localization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / spindle / rRNA processing / chromosome / double-stranded DNA binding / mitochondrial matrix / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase PIN4 / 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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Simulated annealing method starting with an extended strand
Model type detailsminimized average
AuthorsTerada, T. / Shirouzu, M. / Fukumori, Y. / Fujimori, F. / Ito, Y. / Kigawa, T. / Yokoyama, S. / Uchida, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structure of the human parvulin-like peptidyl prolyl cis/trans isomerase, hPar14.
Authors: Terada, T. / Shirouzu, M. / Fukumori, Y. / Fujimori, F. / Ito, Y. / Kigawa, T. / Yokoyama, S. / Uchida, T.
History
DepositionAug 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL PROLYL CIS/TRANS ISOMERASE (PPIASE)


Theoretical massNumber of molelcules
Total (without water)11,3301
Polymers11,3301
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #20minimized average structure

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Components

#1: Protein PEPTIDYL PROLYL CIS/TRANS ISOMERASE (PPIASE)


Mass: 11330.182 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-131 / Mutation: A28G, Q29S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LUNG / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y237

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 3D triple resonance techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM hPar14 U-15N,13C; 20mM sodium phosphate buffer; 100mM NaCl; 5mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
22mM hPar14 U-15N; 20mM sodium phosphate buffer; 100mM NaCl; 5mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Azara2Boucher, W.processing
ANSIG3.3Kraulis, P.J.data analysis
X-PLOR3.1Brunger, A.T.structure solution
X-PLOR3.1Brunger, A.T.refinement
RefinementMethod: Simulated annealing method starting with an extended strand
Software ordinal: 1
Details: Floating chirality method was used to determine the structure of prochiral methylenes and methyls.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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