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- PDB-2kvc: Solution structure of the Mycobacterium tuberculosis protein Rv05... -

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Basic information

Entry
Database: PDB / ID: 2kvc
TitleSolution structure of the Mycobacterium tuberculosis protein Rv0543c, a member of the DUF3349 superfamily. Seattle Structural Genomics Center for Infectious Disease target MytuD.17112.a
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / tuberculosis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyDUF3349, helical bundle / Protein of unknown function DUF3349 / Protein of unknown function (DUF3349) / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / DUF3349 domain-containing protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Kim, C.Y. / Terwilliger, T.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Arch.Biochem.Biophys. / Year: 2011
Title: Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c.
Authors: Buchko, G.W. / Phan, I. / Myler, P.J. / Terwilliger, T.C. / Kim, C.Y.
History
DepositionMar 12, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,6081
Polymers11,6081
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)15 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative uncharacterized protein


Mass: 11608.073 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25177 / H37Ra / Gene: MRA_0550, Rv0543c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21PRO / References: UniProt: A5TZS3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D C(CO)NH
1413D HN(COCA)CB
1513D HNCO
1612D 1H-13C HSQC
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1922D 1H-15N HSQC
11013D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM Rv0543c, 300 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O93% H2O/7% D2O
21-2 mM Rv0543c, 300 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mMRv0543c1-21
300 mMsodium chloride1
20 mMTRIS1
1 mMDTT1
mMRv0543c1-22
300 mMsodium chloride2
20 mMTRIS2
1 mMDTT2
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian UnityPlusVarianUNITYPLUS5003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, P. et al.structure solution
Felix2007Accelrys Software Inc.processing
Sparky3.115Goddard, T. et al.data analysis
PSVS1.1Bhattacharya, A. et al.data analysis
CNS1.1Brunger, A. et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 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 ...Details: 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 1% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS. FROM THIS SET OF 20 STRUCTURES 15 STRUCTURES WITH THE FEWEST/FURTHEST CLOSE CONTACTS WERE SELECTED AND SUBMITTED.
NMR constraintsNOE constraints total: 1118 / NOE intraresidue total count: 364 / NOE long range total count: 241 / NOE medium range total count: 209 / NOE sequential total count: 304 / Hydrogen bond constraints total count: 66 / Protein other angle constraints total count: 132 / Protein phi angle constraints total count: 66 / Protein psi angle constraints total count: 66
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 15

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