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- PDB-2m72: Solution structure of uncharacterized thioredoxin-like protein PG... -

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Basic information

Entry
Database: PDB / ID: 2m72
TitleSolution structure of uncharacterized thioredoxin-like protein PG_2175 from Porphyromonas gingivalis
ComponentsUncharacterized thioredoxin-like protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / THIOREDOXIN-LIKE / New York Structural Genomics Research Consortium / NYSGRC / PSI-Biology
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity
Similarity search - Function
Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin domain-containing protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodSOLUTION NMR / simulating annealing
Model detailslowest energy, model1
AuthorsHarris, R. / Ahmed, M. / Attonito, J. / Bonanno, J.B. / Chamala, S. / Chowdhury, S. / Evans, B. / Fiser, A. / Glenn, A.S. / Hammonds, J. ...Harris, R. / Ahmed, M. / Attonito, J. / Bonanno, J.B. / Chamala, S. / Chowdhury, S. / Evans, B. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Seidel, R.D. / Stead, M. / Girvin, M.E. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Solution structure of uncharacterized thioredoxin-like protein PG_2175 from Porphyromonas gingivalis
Authors: Harris, R. / Ahmed, M. / Attonito, J. / Bonanno, J.B. / Chamala, S. / Chowdhury, S. / Evans, B. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, ...Authors: Harris, R. / Ahmed, M. / Attonito, J. / Bonanno, J.B. / Chamala, S. / Chowdhury, S. / Evans, B. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Seidel, R.D. / Stead, M. / Girvin, M.E. / Almo, S.C.
History
DepositionApr 16, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: 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 / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized thioredoxin-like protein


Theoretical massNumber of molelcules
Total (without water)17,3801
Polymers17,3801
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 / 10020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized thioredoxin-like protein


Mass: 17379.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_2175 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7MT23

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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 3Ds were collected as NUS (30%) using the MDDNMR approach

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Sample preparation

Details
Solution-IDContentsSolvent system
110mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA90% H2O/10% D2O
210mM Na acetate buffer pH 4.5, 3mM DTT, 0.1mM EDTA100% D2O
Sample conditionsIonic strength: 10 / pH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger A. T. et.al.structure calcuation
ARIA2.3Linge, O'Donoghue and Nilgesstructure calcuation
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.32Schwieters, Kuszewski, Tjandra and Clorerefinement
CCPN_Analysis2.2CCPNdata analysis
CCPN_Analysis2.2CCPNchemical shift assignment
MddNMR2.2(MDDNMR) Orekhov, Jaravine, Kazimierczukcollection
MddNMR2.2(MDDNMR) Orekhov, Jaravine, Kazimierczukprocessing
MDDGUI(MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmithcollection
MDDGUI(MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmithprocessing
NMRPipe7.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SideRHansendata analysis
VnmrJ2.2DVariancollection
TopSpin2.1Bruker Biospincollection
MolProbityRichardsondata analysis
CNSrefinement
RefinementMethod: simulating annealing / Software ordinal: 1 / Details: Refinement in a box of water using XPLOR-NIH
NMR constraintsNOE constraints total: 2282 / NOE intraresidue total count: 612 / NOE long range total count: 663 / NOE medium range total count: 422 / NOE sequential total count: 585 / Hydrogen bond constraints total count: 90 / Protein chi angle constraints total count: 12 / Protein other angle constraints total count: 22 / Protein phi angle constraints total count: 87 / Protein psi angle constraints total count: 87
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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