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- PDB-2k36: Structure ensemble Backbone and side-chain 1H, 13C, and 15N Chemi... -

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Basic information

Entry
Database: PDB / ID: 2k36
TitleStructure ensemble Backbone and side-chain 1H, 13C, and 15N Chemical Shift Assignments, 1H-15N RDCs and 1H-1H nOe restraints for protein K7 from the Vaccinia virus
ComponentsProtein K7
KeywordsVIRAL PROTEIN / PROTEIN
Function / homology
Function and homology information


protein sequestering activity / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm
Similarity search - Function
Orthopoxvirus, Protein K7 / dsDNA poxvirus / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / Apoptosis Regulator Bcl-x / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesVaccinia virus
MethodSOLUTION NMR / simulated annealing, simulated annealing
AuthorsKalverda, A.P. / Thompson, G.S. / Vogel, A. / Schr der, M. / Bowie, A.G. / Khan, A.R. / Homans, S.W.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Poxvirus K7 protein adopts a Bcl-2 fold: biochemical mapping of its interactions with human DEAD box RNA helicase DDX3.
Authors: Kalverda, A.P. / Thompson, G.S. / Vogel, A. / Schroder, M. / Bowie, A.G. / Khan, A.R. / Homans, S.W.
History
DepositionApr 22, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein K7


Theoretical massNumber of molelcules
Total (without water)17,4891
Polymers17,4891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 500structures with the lowest energy (tangled structures excluded)
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein K7


Mass: 17488.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: WR Western Reserve / WR
Description: the pET15 vector was modified to replace the thrombin cleavage site with an rTEV cleavage site
Gene: K7R / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P68466

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HNCO
1713D HNHA
1823D 1H-15N NOESY
1913D CBCA(CO)NH
11012D 1H-13C constant time aromatic selected HSQC
11113D (H)CCH-TOCSY
11213D (H)CCH-TOCSY
11312D HB(CBCGCD)HD
11412D HB(CBCGCDCE)HE
11513D 1H-13C NOESY
11622D j MODULATED 1H-15N HSQC
11712D 1H-(13C)-1H aromatic optimised 13C filtered (HSQC) NOESY
NMR detailsText: The structure was determined using a combination of TALOS dihedral, 1H-1H nOe and residual dipolar coupling restraints

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-13C; U-15N] K7D8, 10 mM sodium phosphate, 100 mM sodium chloride, 10 mM DTT, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-15N] K7D8, 10 mM sodium phosphate, 100 mM sodium chloride, 10 mM DTT, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-15N] K7D8, 10 mM sodium phosphate, 100 mM sodium chloride, 10 mM DTT, 0.1 mM DSS, 12 mg/ml Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMK7D8[U-13C; U-15N]1
10 mMsodium phosphate1
100 mMsodium chloride1
10 mMDTT1
0.1 mMDSS1
0.8 mMK7D8[U-15N]2
10 mMsodium phosphate2
100 mMsodium chloride2
10 mMDTT2
0.1 mMDSS2
0.8 mMK7D8[U-15N]3
10 mMsodium phosphate3
100 mMsodium chloride3
10 mMDTT3
0.1 mMDSS3
12 mg/mLPf1 phage3
Sample conditionsIonic strength: 122.5 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRPipe2.5 Rev 2006.184.15.37Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ccpn_analysis1.0.9-1.0.15CCPNdata analysis
ccpn_analysis1.0.9-1.0.15CCPNstructure solution
X-PLOR NIH2.17Schwieters, Kuszewski, Tjandra and Clorestructure solution
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
NMRView5.22Johnson, One Moon Scientificdata analysis
RefinementMethod: simulated annealing, simulated annealing / Software ordinal: 1
Details: PASD/MARVIN with TALOS restraints with p>= 0.9 carried over to Aria 2.1 refinement calculation, Aria 2.1 with TALOS nOe and RDC (VEAN/SANI) restraints All cooling steps exended by a factor of 4 from defaults
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy (tangled structures excluded)
Conformers calculated total number: 500 / Conformers submitted total number: 15

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