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- PDB-6mza: Solution NMR structure of a putative thioredoxin (trxA) in the re... -

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Basic information

Entry
Database: PDB / ID: 6mza
TitleSolution NMR structure of a putative thioredoxin (trxA) in the reduced state from Rickettsia prowazekii, the etiological agent responsible for typhus. Seattle Structural Genomics Center for Infectious Disease target RiprA.00029.a
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / INFECTIOUS DISEASES / SSGCID / typhus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyThioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / protein-disulfide reductase activity / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Thioredoxin
Function and homology information
Biological speciesRickettsia prowazekii (bacteria)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200025C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700057C United States
CitationJournal: To Be Published
Title: Solution NMR structure of reduced Rickettsia prowazekii thioredoxin.
Authors: Buchko, G.W. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionNov 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 2.0Dec 4, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Polymer sequence
Category: entity_poly / pdbx_SG_project ...entity_poly / pdbx_SG_project / pdbx_database_related / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _entity_poly.pdbx_target_identifier / _pdbx_database_status.SG_entry ..._entity_poly.pdbx_target_identifier / _pdbx_database_status.SG_entry / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2May 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: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)15,2871
Polymers15,2871
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion chromatography suggests it is a monomer in solution.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Thioredoxin / / Trx


Mass: 15287.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia prowazekii (strain Madrid E) (bacteria)
Strain: Madrid E / Gene: trxA, RP002 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZEE0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HNCA
141isotropic13D C(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CA)CO
191isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aromatic
171isotropic13D 1H-13C NOESY aliphatic
1103isotropic1DEUTERIUM EXCHANGE
1111isotropic12D 1H-13C HSQC
1122isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 0.8 mM [U-99% 13C; U-99% 15N] R29, 93% H2O/7% D2ODouble-labeledSample_193% H2O/7% D2O
solution2100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 0.5 mM [U-10% 13C; U-100% 15N] R29, 93% H2O/7% D2OSample_293% H2O/7% D2O
solution3100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 0.5 mM [U-99% 15N] R29, 100% D2OSample_3100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance1
1 mMDTTnatural abundance1
0.8 mMR29[U-99% 13C; U-99% 15N]1
100 mMsodium chloridenatural abundance2
20 mMTRISnatural abundance2
1 mMDTTnatural abundance2
0.5 mMR29[U-10% 13C; U-100% 15N]2
100 mMsodium chloridenatural abundance3
20 mMTRISnatural abundance3
1 mMDTTnatural abundance3
0.5 mMR29[U-99% 15N]3
Sample conditionsIonic strength: 0.12 M / Label: cond_1 / pH: 7 / PH err: 0.2 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.5

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger A. T. et.al.refinement
TALOS+Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Sparky3.13Goddarddata analysis
PSVS1.5Bhattacharya and Montelionedata analysis
Sparky3.13Goddardpeak picking
Refinement
MethodSoftware ordinalDetails
torsion angle dynamics2STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW
simulated annealing1refinement in explicit water. Oberserved clashes due to this refinement process.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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