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- PDB-6amr: Solution NMR structure of a putative thioredoxin (ECH_0218) in th... -

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Basic information

Entry
Database: PDB / ID: 6amr
TitleSolution NMR structure of a putative thioredoxin (ECH_0218) in the reduced state from Ehrlichia chaffeensis, the etiological agent responsible for human monocytic ehrlichiosis. Seattle Structural Genomics Center for Infectious Disease target EhchA.00546.a
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / INFECTIOUS DISEASES / SSGCID / TICK DISEASES / 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 speciesEhrlichia chaffeensis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
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: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Solution NMR structures of oxidized and reduced Ehrlichia chaffeensis thioredoxin: NMR-invisible structure owing to backbone dynamics.
Authors: Buchko, G.W. / Hewitt, S.N. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 11, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionSep 20, 2017ID: 2MCS
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 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:
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Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)14,3621
Polymers14,3621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Protein was a monomer via SEC.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8090 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Thioredoxin


Mass: 14362.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas) (bacteria)
Strain: ATCC CRL-10679 / Arkansas / Gene: trx, ECH_0218 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-PRARE2 / References: UniProt: Q2GHP2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic32D 1H-15N HSQC
121anisotropic32D 1H-13C HSQC aliphatic
131anisotropic32D 1H-13C HSQC aromatic
141anisotropic13D C(CO)NH
151anisotropic13D HN(CA)CB
1111anisotropic13D HNCO
1101anisotropic33D 1H-15N NOESY
191anisotropic23D 1H-13C NOESY aliphatic
181anisotropic23D 1H-13C NOESY aromatic
171anisotropic22D 1H-15N HSQC Deuterium Exchange

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Sample preparation

DetailsType: solution
Contents: 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O
Label: Sample_1 / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance1
1 mMDTTnatural abundance1
Sample conditionsIonic strength: 0.12 M / Ionic strength err: 0.003 / Label: Condition_1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS6001
Varian VXRSVarianVXRS7502
Varian VXRSVarianVXRS8003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger A. T. et.al.refinement
Sparky3.115Goddarddata analysis
PSVS1.5Bhattacharya and Montelionedata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
TALOS+Cornilescu, Delaglio and Baxdata analysis
Felix2007Accelrys Software Inc.processing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 4
Details: Proline-97 was constrained to the Cis configuration on the basis of other Trx structures. STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL ...Details: Proline-97 was constrained to the Cis configuration on the basis of other Trx structures. STRUCTURE 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 10% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS.
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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