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- PDB-2kq9: Solution structure of DnaK suppressor protein from Agrobacterium ... -

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Basic information

Entry
Database: PDB / ID: 2kq9
TitleSolution structure of DnaK suppressor protein from Agrobacterium tumefaciens C58. Northeast Structural Genomics Consortium target AtT12/Ontario Center for Structural Proteomics Target atc0888
ComponentsDnaK suppressor protein
KeywordsTRANSCRIPTION / Zinc binding protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


DksA, coiled-coil domain / DksA, N-terminal domain superfamily / Zinc finger, DksA/TraR C4-type / Prokaryotic dksA/traR C4-type zinc finger / Prokaryotic dksA C4-type zinc finger profiles. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DnaK suppressor protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
Citation
Journal: To be Published
Title: Solution Structure of DnaK protein from Agrobacterium tumefaciens C58. Northeast Structural Genomics Consortium target AtT12/Ontario Center for Structural Proteomics Target atc0888
Authors: Wu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Montelione, G.T. / Arrowsmith, C.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionNov 2, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaK suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7022
Polymers12,6361
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DnaK suppressor protein


Mass: 12636.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Strain: C58 / ATCC 33970 / Gene: dskA, Atu0905 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UGY0*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D C(CO)NH
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D 1H-13C NOESY aromatic
11222D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] atc0888, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-7% 13C; U-100% 15N] atc0888, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMatc0888-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
10 uMzinc sulphate-41
10 mMDTT-5[U-100% 2H]1
10 mMbenzamidine-61
1 %inhibitor cocktail-71
0.5 mMatc0888-8[U-7% 13C; U-100% 15N]2
10 mMTRIS-9[U-100% 2H]2
300 mMsodium chloride-102
10 uMzinc sulphate-112
10 mMDTT-12[U-100% 2H]2
10 mMbenzamidine-132
1 %inhibitor cocktail-142
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas Arrowsmithprocessing
Sparky3.95Goddarddata analysis
Sparky3.95Goddardpeak picking
FAWN1Lemak and Arrowsmithchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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