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- PDB-2hgc: Solution NMR structure of the YjcQ protein from Bacillus subtilis... -

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Basic information

Entry
Database: PDB / ID: 2hgc
TitleSolution NMR structure of the YjcQ protein from Bacillus subtilis. Northeast Structural Genomics target SR346.
ComponentsYjcQ protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR346 / AutoStructure / NESG / PSI-2 / Northeast Structural Genomics Consortium / Protein Structure Initiative
Function / homologyBacteriophage Tuc2009, YjcQ / YjcQ protein / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YjcQ
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / Noesy assignments made with iterative method using CS, 3J, Hyper (dihedral), and Dyana for simulated annealing MD. Converged structures are further refined using NIH-xplor, CNS in explicit water shell (Nielges) . Full lenght sequence was carried through the refinement protocol, the disordered regions, hexHIS tag are not reported. Structure based on 595 constraints, 249 long range, 163 dihedral constraints, 36 H-bond constraints.
AuthorsRossi, P. / Cort, J.R. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. ...Rossi, P. / Cort, J.R. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the YjcQ protein from Bacillus subtilis. Northeast Structural Genomics target SR346. (CASP Target)
Authors: Rossi, P. / Cort, J.R. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Kennedy, M.A. / Montelione, G.T.
History
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 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: YjcQ protein


Theoretical massNumber of molelcules
Total (without water)12,1151
Polymers12,1151
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein YjcQ protein


Mass: 12114.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yjcQ / Plasmid: SR346_21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: O31639

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131(H)CCH-TOCSY, (H)CCH-COSY,CC(CO)NH-TOCSY
1413D-HN(CA)CB, HN(CO)CACB, HBHA(CO)NH, HNCO
252C13 HSQC noct Stereospecific VL Me assign.
161Het-NOE, T1/T1rho
NMR detailsText: Structure determined by Triple resonance NMR spectroscopy. Monomer in solution by NMR Tc = 8.6 +/- 0.1 ns (1D T1/T1rho +/- fit std). CIS peptide res. 19T-20P. Structure determined by triple ...Text: Structure determined by Triple resonance NMR spectroscopy. Monomer in solution by NMR Tc = 8.6 +/- 0.1 ns (1D T1/T1rho +/- fit std). CIS peptide res. 19T-20P. Structure determined by triple resonance NMR spectroscopy. Coordinates reported from residue 5 to 82 section based on order parameter. AutoAssign used for backbone assignment, manually completed sidechain. 13C and 15N NOESY were assigned with AutoStructure. Dihedral angle restraints determined by HYPER . Assignment stats (excluding C-term tag): backbone 84.6%, sidechain 74.7%, aromatic (sc) 89.36%, VL methyl stereospecific 100%, unambiguous sidechain NH2 85.7%. Structure quality factor PSVS 1.3: ordered residues ranges alpha helix (7-17, 23-26,30-43, 67-76), b-strand (46-47, 64-65, 50-51, 56-57) [S(phi)+S(psi)]>1.8. RMSD 0.6 bb, 1.2 all heavy atoms. Rama: 95.8% most fav, 3.7% addtl. all., 0.3 gen. all.,0.3% disall. Procheck (psi-phi): 0.03/0.43 (raw/Z), Procheck (all): 1.18/-1.18 (raw/Z), MolProbity Clash: 27.67/-3.22 (raw/Z). RPF scores all assigned residues (fit of noesy peaklists to structure): Recall: 0.896, Precision: 0.90, F-measure: 0.898, DP-score: 0.70. Monomer by light scattering.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.85 mM U-13C,15N SR346, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN35% D2O, 95% H2O
20.77 mM 5%-13C,U-15N SR346, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN35% D2O, 95% H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 M NaCl 5.5atmospheric atm293 K
20.1 M NaCl 5.5atmospheric atm293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
XwinNMR3.5Bruker Biospincollection
DYANA1.2Gunthertstructure solution
X-PLOR2.11.2Clorerefinement
NMRPipe2005Delaglioprocessing
Sparky3.11Goddard & Knellerdata analysis
AutoAssign2.2.1Zimmerman, Moseley, Montelionedata analysis
AutoStructure2.1.1Huang, Montelionestructure solution
HYPER2.1Tejero, Montelionestructure solution
PdbStat4.1Tejero, Montelionedata analysis
PSVS1.3Bhattacharya, Montelionerefinement
Procheck NMR3.51Laskowski, MacArthurrefinement
MolProbity3.01Lovell, Richardson et. al.refinement
RefinementMethod: Noesy assignments made with iterative method using CS, 3J, Hyper (dihedral), and Dyana for simulated annealing MD. Converged structures are further refined using NIH-xplor, CNS in explicit ...Method: Noesy assignments made with iterative method using CS, 3J, Hyper (dihedral), and Dyana for simulated annealing MD. Converged structures are further refined using NIH-xplor, CNS in explicit water shell (Nielges) . Full lenght sequence was carried through the refinement protocol, the disordered regions, hexHIS tag are not reported. Structure based on 595 constraints, 249 long range, 163 dihedral constraints, 36 H-bond constraints.
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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