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- PDB-2l5o: Solution Structure of a Putative Thioredoxin from Neisseria menin... -

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Basic information

Entry
Database: PDB / ID: 2l5o
TitleSolution Structure of a Putative Thioredoxin from Neisseria meningitidis
ComponentsPutative thioredoxin
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / NYSGRC / PSI-Biology / TRANSPORT PROTEIN OXIDOREDUCTASE / New York Structural Genomics Research Consortium
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 thioredoxin
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (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. ...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. / New York SGX Research Center for Structural Genomics (NYSGXRC) / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Solution Structure of a Putative Thioredoxin from Neisseria meningitidis
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
DepositionNov 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 8, 2013Group: Structure summary
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 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 thioredoxin


Theoretical massNumber of molelcules
Total (without water)17,0461
Polymers17,0461
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 thioredoxin


Mass: 17046.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: NMB1958 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JXN4

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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

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] putative thioredoxin, 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM putative thioredoxin, 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMputative thioredoxin-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
1 mMDTT-41
1 mMputative thioredoxin-52
20 mMsodium phosphate-62
100 mMsodium chloride-72
1 mMDTT-82
Sample conditionsIonic strength: 100 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger A. T. et.al.refinement
CCPN_Analysis2.1.2CCPNdata analysis
RefinementMethod: simulating annealing / Software ordinal: 1 / Details: Refinement in a box of water
NMR constraintsNOE constraints total: 1813 / NOE intraresidue total count: 579 / NOE long range total count: 508 / NOE medium range total count: 270 / NOE sequential total count: 418 / Hydrogen bond constraints total count: 45 / Protein phi angle constraints total count: 97 / Protein psi angle constraints total count: 97
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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