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- PDB-2rn7: NMR solution structure of TnpE protein from Shigella flexneri. No... -

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Basic information

Entry
Database: PDB / ID: 2rn7
TitleNMR solution structure of TnpE protein from Shigella flexneri. Northeast Structural Genomics Target SfR125
ComponentsIS629 orfA
KeywordsUNKNOWN FUNCTION / helix / all alpha / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


transposase activity / DNA transposition / DNA binding
Similarity search - Function
Transposase IS3/IS911family / Transposase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IS629 orfA / IS629 orfA
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, water refinement
Model detailsall alpha
AuthorsRamelot, T.A. / Cort, J.R. / Semesi, A. / Garcia, M. / Yee, A.A. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of TnpE protein from Shigella flexneri. Northeast Structural Genomics Target SfR125
Authors: Ramelot, T.A. / Cort, J.R. / Semesi, A. / Garcia, M. / Yee, A. / Arrowsmith, C.H. / Kennedy, M.A.
History
DepositionDec 8, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IS629 orfA


Theoretical massNumber of molelcules
Total (without water)12,6621
Polymers12,6621
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 / 25structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein IS629 orfA


Mass: 12662.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: tnpE / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pMGK / References: UniProt: Q7UDG6, UniProt: A0A0H2VTH7*PLUS
Sequence detailsTHERE ARE CONFLICTS BETWEEN SEQRES(LEU A 92) AND SEQUENCE DATABASE (GLN). THE AUTHORS BELIEVE THAT ...THERE ARE CONFLICTS BETWEEN SEQRES(LEU A 92) AND SEQUENCE DATABASE (GLN). THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: all alpha
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D HBHA(CO)NH
1713D C(CO)NH
1813D (H)CCH-TOCSY
1913D (H)CCH-TOCSY
11012D 1H-15N HSQC
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliph
11313D 1H-13C NOESY arom
11413D (H)CCH-COSY
11512D 1H-13C HSQC
11622D 1H-15N HSQC
11722D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-100% 13C; U-100% 15N] TnpE protein, 10mM TRIS, 500mM sodium chloride, 10mM DTT, 0.01mM Zn+2, 0.01% sodium azide, 1mM benzamidine, 1x protease inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
21mM [U-7% 13C; U-100% 15N] TnpE protein, 10mM TRIS, 500mM sodium chloride, 10mM DTT, 0.01mM Zn+2, 0.01% sodium azide, 1mM benzamidine, 1x protease inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTnpE protein[U-100% 13C; U-100% 15N]1
10 mMTRIS1
500 mMsodium chloride1
10 mMDTT1
0.01 mMZn+21
0.01 %sodium azide1
1 mMbenzamidine1
1 %protease inhibitor cocktail1
1 mMTnpE protein[U-7% 13C; U-100% 15N]2
10 mMTRIS2
500 mMsodium chloride2
10 mMDTT2
0.01 mMZn+22
0.01 %sodium azide2
1 mMbenzamidine2
1 %protease inhibitor cocktail2
Sample conditionsIonic strength: 0.5 / pH: 7.7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipenmrpipe_linuxDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
AutoStructure2.1.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.1Goddarddata analysis
RefinementMethod: DGSA-distance geometry simulated annealing, water refinement
Software ordinal: 1 / Details: Xplor-NIH, CNS
NMR constraintsNOE constraints total: 351 / NOE intraresidue total count: 9 / NOE long range total count: 89 / NOE medium range total count: 153 / NOE sequential total count: 109 / Hydrogen bond constraints total count: 38 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 41 / Protein psi angle constraints total count: 41
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 25 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0.9 ° / Maximum upper distance constraint violation: 0.08 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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