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- PDB-2m46: Solution NMR structure of SACOL0876 from Staphylococcus aureus CO... -

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Basic information

Entry
Database: PDB / ID: 2m46
TitleSolution NMR structure of SACOL0876 from Staphylococcus aureus COL, NESG target ZR353 and CSGID target IDP00841
ComponentsArsenate reductase, putative
KeywordsOXIDOREDUCTASE / pathogenic bacterial protein / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Arsenate reductase, putative / Arsenate reductase, putative
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Yee, A. / Houliston, S. / Garcia, M. / Savchenko, A. / Arrowsmith, C.H. / Anderson, W.F. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP) / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Solution NMR structure of SACOL0876 from Staphylococcus aureus COL, NESG target ZR353 and CSGID target IDP00841
Authors: Wu, B. / Yee, A. / Houliston, S. / Garcia, M. / Savchenko, A. / Arrowsmith, C.H.
History
DepositionJan 29, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Structure summary
Revision 1.2Jun 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
Revision 1.3May 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: Arsenate reductase, putative


Theoretical massNumber of molelcules
Total (without water)16,3631
Polymers16,3631
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Arsenate reductase, putative


Mass: 16362.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: COL / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HHK9, UniProt: A0A0H2WW65*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C NOESY aromatic
11023D 1H-13C NOESY
11132D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 13C; U-100% 15N] SACOL0876, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-100% 13C; U-100% 15N] SACOL0876, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 x inhibitor cocktail, 99% D2O99% D2O
30.2 mM [U-7% 13C; U-100% 15N] SACOL0876, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMSACOL0876-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
10 mMDTT-4[U-100% 2H]1
0.01 %NaN3-51
10 mMbenzamidine-61
1 %inhibitor cocktail-71
0.3 mMSACOL0876-8[U-100% 13C; U-100% 15N]2
10 mMTRIS-9[U-100% 2H]2
300 mMsodium chloride-102
10 mMDTT-11[U-100% 2H]2
0.01 %NaN3-122
10 mMbenzamidine-132
1 %inhibitor cocktail-142
0.2 mMSACOL0876-15[U-7% 13C; U-100% 15N]3
10 mMTRIS-16[U-100% 2H]3
300 mMsodium chloride-173
10 mMDTT-18[U-100% 2H]3
0.01 %NaN3-193
10 mMbenzamidine-203
1 %inhibitor cocktail-213
Sample conditionsIonic strength: 300 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas, Arrowsmithprocessing
Sparky3.95Goddarddata analysis
FMCGUI2.4Lemak, Arrowsmithchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
FAWNLemak, Arrowsmithchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2926 / NOE intraresidue total count: 517 / NOE long range total count: 1031 / NOE medium range total count: 804 / NOE sequential total count: 574 / Hydrogen bond constraints total count: 82 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 91 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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