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- PDB-2kta: Solution NMR structure of a domain of protein A6KY75 from Bactero... -

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Basic information

Entry
Database: PDB / ID: 2kta
TitleSolution NMR structure of a domain of protein A6KY75 from Bacteroides vulgatus, Northeast Structural Genomics target BvR106A
ComponentsPutative helicase
KeywordsHYDROLASE / PSI / NESG / GFT NMR / ATP-binding / Nucleotide-binding / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


helicase activity / DNA binding / ATP binding
Similarity search - Function
Helix Hairpins - #530 / Helicase-associated / Helicase associated domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helix Hairpins / Helix non-globular / Helicase conserved C-terminal domain / Special / Superfamilies 1 and 2 helicase C-terminal domain profile. ...Helix Hairpins - #530 / Helicase-associated / Helicase associated domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helix Hairpins / Helix non-globular / Helicase conserved C-terminal domain / Special / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesBacteroides vulgatus (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsMills, J.L. / Sukumaran, D.K. / Sathyamoorthy, B. / Belote, R.L. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Swapna, G.V.T. / Everett, J.K. ...Mills, J.L. / Sukumaran, D.K. / Sathyamoorthy, B. / Belote, R.L. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Swapna, G.V.T. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of a domain of protein A6KY75 from Bacteroides vulgatus, Northeast Structural Genomics target BvR106A
Authors: Mills, J.L. / Sukumaran, D.K. / Sathyamoorthy, B. / Belote, R.L. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Swapna, G.V.T. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionJan 26, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references / Structure summary
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 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: Putative helicase


Theoretical massNumber of molelcules
Total (without water)9,1181
Polymers9,1181
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative helicase


Mass: 9117.504 Da / Num. of mol.: 1 / Fragment: sequence database residues 627-693
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_0683, BVU_1551 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: A6KY75

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
131(4,3)D GFT CABCA(CO)NH
141(4,3)D GFT HNCABCA
151(4,3)D GFT HABCAB(CO)NH
1613D (H)CCH-TOCSY
1713D simultaneous NOESY
1813D 1H-15N NOESY

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Sample preparation

DetailsContents: 1.11 mM [U-99% 13C; U-99% 15N] BvR106A, 10 v/v [U-2H] D2O, 90 v/v H2O, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 w/v sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.11 mMBvR106A-1[U-99% 13C; U-99% 15N]1
10 v/vD2O-2[U-2H]1
90 v/vH2O-31
20 mMMES-41
100 mMsodium chloride-51
5 mMcalcium chloride-61
10 mMDTT-71
50 uMDSS-81
0.02 w/vsodium azide-91
Sample conditionsIonic strength: 235 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian UnityPlus / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CSIWishart and Sykesstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
CYANAHerrmann, Guntert and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
MOLMOLKoradi, Billeter and Wuthrichrefinement
PSVSBhattacharya and Montelionerefinement
PROSAGuntertprocessing
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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