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- PDB-2djk: Solution structure of the b' domain of thermophilic fungal protei... -

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Basic information

Entry
Database: PDB / ID: 2djk
TitleSolution structure of the b' domain of thermophilic fungal protein disulfide isomerase
ComponentsProtein disulfide-isomerase
KeywordsISOMERASE / thioredoxin fold
Function / homology
Function and homology information


protein disulfide-isomerase / protein disulfide isomerase activity / endoplasmic reticulum lumen
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein disulfide-isomerase
Similarity search - Component
Biological speciesHumicola insolens (fungus)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsKato, K. / Yamaguchi, Y.
CitationJournal: To be Published
Title: Solution structure of the b' domain of thermophilic fungal protein disulfide isomerase
Authors: Nakano, M. / Maeno, A. / Sasakawa, H. / Yamaguchi, Y. / Kikuchi, J. / Asami, O. / Kajino, T. / Kato, K.
History
DepositionApr 4, 2006Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 25, 2006ID: 1V52
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 1.4May 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: Protein disulfide-isomerase


Theoretical massNumber of molelcules
Total (without water)14,5051
Polymers14,5051
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein disulfide-isomerase / PDI


Mass: 14505.343 Da / Num. of mol.: 1 / Fragment: b' domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humicola insolens (fungus) / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55059, protein disulfide-isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1322D NOESY
1431H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM protein disulfide isomerase b' domain U-15N,13C; 10mM sodium phosphate buffer,100mM KCl, 10mM ditiothreitol; 90% H2O,10% D2O90% H2O/10% D2O
21.0mM protein disulfide isomerase b' domain; 10mM sodium phosphate buffer,100mM KCl, 10mM ditiothreitol; 99% D2O99% D2O
30.3mM protein disulfide isomerase b' domain U-15N; 10mM sodium phosphate buffer, 10mM ditiothreitol, 10mg/ml Pf1 phage; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 0.16 / pH: 6 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
JEOL ECAJEOLECA9201
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6collection
Delta4.3.3collection
XwinNMR2.6processing
Sparky3.1Goddard and Knellerdata analysis
CYANA2.1Guntertstructure solution
CNS1.1refinement
RefinementMethod: distance geometry 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: 10

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