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- PDB-2lja: Solution Structure of a putative thiol-disulfide oxidoreductase f... -

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Basic information

Entry
Database: PDB / ID: 2lja
TitleSolution Structure of a putative thiol-disulfide oxidoreductase from Bacteroides vulgatus
ComponentsPutative thiol-disulfide oxidoreductase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / THIOREDOXIN-LIKE / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
: / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative thiol-disulfide oxidoreductase
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodSOLUTION NMR / simulating annealing
Model detailslowest energy, model 1
AuthorsHarris, R. / Seidel, R.D. / Hillerich, B. / Gizzi, A. / Kar, A. / Lafleur, J. / Chamala, S. / Foti, R. / Villegas, G. / Evans, B. ...Harris, R. / Seidel, R.D. / Hillerich, B. / Gizzi, A. / Kar, A. / Lafleur, J. / Chamala, S. / Foti, R. / Villegas, G. / Evans, B. / Zencheck, W. / Girvin, M.E. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Solution Structure of a putative thiol-disulfide oxidoreductase from Bacteroides vulgatus
Authors: Harris, R. / Seidel, R.D. / Hillerich, B. / Gizzi, A. / Kar, A. / Lafleur, J. / Chamala, S. / Foti, R. / Villegas, G. / Evans, B. / Zencheck, W. / Girvin, M.E. / Almo, S.C.
History
DepositionSep 9, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 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

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Assembly

Deposited unit
A: Putative thiol-disulfide oxidoreductase


Theoretical massNumber of molelcules
Total (without water)17,1841
Polymers17,1841
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)20 / 10020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative thiol-disulfide oxidoreductase


Mass: 17183.678 Da / Num. of mol.: 1 / Fragment: UNP residues 309-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_1977 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6L1T5

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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
16213C aromatic NOESY-HSQC
171HNCO
181HN(CA)CO
191HNCA
1101HN(CO)CA
1111HN(CA)CB
1121CBCA(CO)NH
NMR detailsText: All 3D data were collected with non-uniform sampling

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] putative thiol-disulfide oxidoreductase, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 1 mM EDTA, 10 % [U-100% 2H] D2O, 0.2 mM DSS, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] putative thiol-disulfide oxidoreductase, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 1 mM EDTA, 100 % [U-100% 2H] D2O, 0.2 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMputative thiol-disulfide oxidoreductase-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMDTT-41
1 mMEDTA-51
10 %D2O-6[U-100% 2H]1
0.2 mMDSS-71
1 mMputative thiol-disulfide oxidoreductase-8[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-92
50 mMsodium chloride-102
1 mMDTT-112
1 mMEDTA-122
100 %D2O-13[U-100% 2H]2
0.2 mMDSS-142
Sample conditionsIonic strength: 70 / pH: 5.8 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CCPN_Analysis2.1.5CCPNdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MddNMR1.8Orekhov, Jaravine, Maxim, Kazimiercsukprocessing
MDDGUI1Gutmanas, Arrowsmithprocessing
RefinementMethod: simulating annealing / Software ordinal: 1 / Details: Refinement in a box of water
NMR constraintsNOE constraints total: 2343 / NOE intraresidue total count: 584 / NOE long range total count: 635 / NOE medium range total count: 430 / NOE sequential total count: 610 / Hydrogen bond constraints total count: 76 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 82 / Protein psi angle constraints total count: 81
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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