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- PDB-2kp2: Solution structure of the b' domain of thermophilic fungal protei... -

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Basic information

Entry
Database: PDB / ID: 2kp2
TitleSolution structure of the b' domain of thermophilic fungal protein disulfide isomerase
ComponentsProtein disulfide-isomerase
KeywordsISOMERASE / THIOREDOXIN FOLD / Disulfide bond / Endoplasmic reticulum / Redox-active center
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 / DGSA-distance geometry simulated annealing
Model detailsfewest violations, model 10
AuthorsKato, K. / Yamaguchi, Y. / Serve, O.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Redox-Dependent Domain Rearrangement of Protein Disulfide Isomerase Coupled with Exposure of Its Substrate-Binding Hydrophobic Surface
Authors: Serve, O. / Kamiya, Y. / Maeno, A. / Nakano, M. / Murakami, C. / Sasakawa, H. / Yamaguchi, Y. / Harada, T. / Kurimoto, E. / Yagi-Utsumi, M. / Iguchi, T. / Inaba, K. / Kikuchi, J. / Asami, O. ...Authors: Serve, O. / Kamiya, Y. / Maeno, A. / Nakano, M. / Murakami, C. / Sasakawa, H. / Yamaguchi, Y. / Harada, T. / Kurimoto, E. / Yagi-Utsumi, M. / Iguchi, T. / Inaba, K. / Kikuchi, J. / Asami, O. / Kajino, T. / Oka, T. / Nakasako, M. / Kato, K.
History
DepositionOct 6, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 27, 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

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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
Water0
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 #1fewest violations

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Components

#1: Protein Protein disulfide-isomerase / / PDI


Mass: 14505.343 Da / Num. of mol.: 1 / Fragment: B' Domain, UNP residues 228-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humicola insolens (fungus) / Plasmid: PGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): 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
1122D 1H-1H NOESY
1223D 1H-15N NOESY
1323D 1H-13C NOESY
1412D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM [U-15N] PDI B'-1, 10mM sodium phosphate-2, 100mM potassium chloride-3, 10mM DTT-4, 99 % D2O99% D2O
21.0mM [U-13C; U-15N] PDI B'-5, 10mM sodium phosphate-6, 100mM potassium chloride-7, 10mM DTT-8, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMPDI B'-1[U-15N]1
10 mMsodium phosphate-21
100 mMpotassium chloride-31
10 mMDTT-41
1.0 mMPDI B'-5[U-13C; U-15N]2
10 mMsodium phosphate-62
100 mMpotassium chloride-72
10 mMDTT-82
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
BRUKER DRXBrukerDRX8001
JEOL ECAJEOLECA9202

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Biospincollection
XwinNMR2.6Bruker Biospinprocessing
Delta4.3.3JEOLcollection
Delta4.3.3JEOLprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddardpeak picking
CYANA2.1Guntert, Mumenthaler, Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler, Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2276 / NOE intraresidue total count: 464 / NOE long range total count: 780 / NOE medium range total count: 405 / NOE sequential total count: 627 / Protein phi angle constraints total count: 70 / Protein psi angle constraints total count: 70
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 11.3 ° / Maximum upper distance constraint violation: 1.5 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.07 Å

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