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- PDB-2kuc: Solution Structure of a putative disulphide-isomerase from Bacter... -

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Basic information

Entry
Database: PDB / ID: 2kuc
TitleSolution Structure of a putative disulphide-isomerase from Bacteroides thetaiotaomicron
ComponentsPutative disulphide-isomerase
KeywordsISOMERASE / structural genomics / putative disulphide-isomerase / thioredoxin fold / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


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
Putative disulphide-isomerase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodSOLUTION NMR / simulating annealing
Model detailslowest energy, model 1
AuthorsHarris, R. / Foti, R. / Seidel, R.D. / Bonanno, J.B. / Freeman, J. / Bain, K.T. / Sauder, J.M. / Burley, S.K. / Girvin, M.E. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Solution Structure of a putative disulphide-isomerase from Bacteroides thetaiotaomicron
Authors: Harris, R. / Foti, R. / Seidel, R.D. / Bonanno, J.B. / Freeman, J. / Bain, K.T. / Sauder, J.M. / Burley, S.K. / Girvin, M.E. / Almo, S.C.
History
DepositionFeb 17, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative disulphide-isomerase


Theoretical massNumber of molelcules
Total (without water)14,8281
Polymers14,8281
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)20 / 20020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative disulphide-isomerase


Mass: 14828.109 Da / Num. of mol.: 1 / Fragment: residues 43-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_3069 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A386

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC
12115N NOESY-HSQC
13213C HSQC
142aromatic 13C HSQC
15213C NOESY-HSQC
162aromatic 13C NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] putative disulphide-isomerase, 150 mM sodium chloride, 20 mM sodium phosphate, 90 % H2O, 10 % D2O, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] putative disulphide-isomerase, 150 mM sodium chloride, 20 mM sodium phosphate, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMputative disulphide-isomerase-1[U-13C; U-15N]1
150 mMsodium chloride-21
20 mMsodium phosphate-31
90 %H2O-41
10 %D2O-51
1 mMputative disulphide-isomerase-6[U-13C; U-15N]2
150 mMsodium chloride-72
20 mMsodium phosphate-82
100 %D2O-92
Sample conditionsIonic strength: 150mM NaCl / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Inova / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulating annealing / Software ordinal: 1
Details: RECOORD scripts used - torsion angle dynamincs and refinement in a box of water refinement
NMR constraintsNOE constraints total: 2369 / NOE intraresidue total count: 621 / NOE long range total count: 641 / NOE medium range total count: 456 / NOE sequential total count: 596 / Hydrogen bond constraints total count: 64 / Protein phi angle constraints total count: 92 / Protein psi angle constraints total count: 92
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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