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- PDB-2hjq: NMR Structure of Bacillus Subtilis Protein YqbF, Northeast Struct... -

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Basic information

Entry
Database: PDB / ID: 2hjq
TitleNMR Structure of Bacillus Subtilis Protein YqbF, Northeast Structural Genomics Target SR449
ComponentsHypothetical protein yqbFHypothesis
KeywordsSTRUCTURAL GENOMICS / two-domain / Bsu26130 / YqbF / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


YqbF domain / Uncharacterised protein YqbF domain / YqbF domain superfamily / YqbF, hypothetical protein domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Ribosomal Protein L9; domain 1 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Rho termination factor, N-terminal domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich ...YqbF domain / Uncharacterised protein YqbF domain / YqbF domain superfamily / YqbF, hypothetical protein domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Ribosomal Protein L9; domain 1 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Rho termination factor, N-terminal domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YqbF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / distance geometry simulated annealing, CNS water refinement
AuthorsDing, K. / Ramelot, T.A. / Cort, J.R. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. ...Ding, K. / Ramelot, T.A. / Cort, J.R. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: NMR Structure of Bacillus Subtilis Protein YqbF, Northeast Structural Genomics Target SR449
Authors: Cort, J.R. / Ramelot, T.A. / Xiao, R. / Swapna, G.V.T. / Montelione, G.M. / Kennedy, M.A.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: 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_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 / _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: Hypothetical protein yqbF


Theoretical massNumber of molelcules
Total (without water)12,9361
Polymers12,9361
Non-polymers00
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 / 30structures with the lowest bond energy
RepresentativeModel #1lowest total energy

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Components

#1: Protein Hypothetical protein yqbF / Hypothesis


Mass: 12935.554 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yqbF / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (LAmbda DE3) PMGK / References: UniProt: P45922

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1334D 13C-separated NOESY
NMR detailsText: THE STRUCTURES ARE BASED ON A TOTAL OF 1719 RESTRAINTS. 1536 are NOE-DERIVED; INTRA-RESIDUE [i=j] = 268; SEQUENTIAL [(I-J)=1] = 437 MEDIUM RANGE [10.1 ANG = 0; AVERAGE RMS DISTANCE VIOLATION / ...Text: THE STRUCTURES ARE BASED ON A TOTAL OF 1719 RESTRAINTS. 1536 are NOE-DERIVED; INTRA-RESIDUE [i=j] = 268; SEQUENTIAL [(I-J)=1] = 437 MEDIUM RANGE [1<(I-J)<5] = 387; LONG RANGE [(I-J)>=5] = 444; HYDROGEN BOND RESTRAINTS = 42 (2 PER H-BOND); NUMBER OF NOE RESTRAINTS PER RESIDUE = 16.3 (RESIDES 2-47,57-104); DIHEDRAL-ANGLE RESTRAINTS = 141 (70 PHI, 71 PSI); TOTAL NUMBER OF RESTRAINTS PER RESIDUE = 18.3 (RESIDES 2-47,57-104); NUMBER OF LONG RANGE RESTRAINTS PER RESIDUE = 4.7 NUMBER OF STRUCTURES COMPUTED = 20; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.1 ANG = 0; AVERAGE RMS DISTANCE VIOLATION / CONSTRAINT = 0.06 ANGSTROMS.; MAXIMUM DISTANCE VIOLATION 0.05 ANG. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >10 DEG = 0 MAX DIHEDRAL ANGLE VIOLATION = 0.5 DEG. AVERAGE RMS ANGLE VIOLATION / CONSTRAINT = 0.003 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 2-47 = 0.5 ANG; ALL HEAVY ATOMS = 0.9 ANG (RESIDUES 2-47) RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 2-47 = 0.7 ANG; ALL HEAVY ATOMS = 1.3 ANG (RESIDUES 57-98) PROCHECK (RESIDUES 2-47,57-104): MOST FAVORED REGIONS = 89% ADDITIONAL ALLOWED REGIONS = 10%; GENEROUSLY ALLOWED REGIONS = 0%; DISALLOWED REGIONS = 1%. 6 NON-NATIVE N-TERMINAL RESIDUES (MAGDPL) AND 8 C-TERMINAL RESDIUES, INLUDING THE HIS TAG, (LEHHHHHH) WERE INCLUDED IN THE STRUCTURE CALCULATION.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3mM YqbF, U-N15, 13C; 20 mM NH4OAc, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 95% H2O, 5% D2O95% H2O/5% D2O
20.7mM YqbF, U-N15, 5% 13C; 20 mM NH4OAc, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 95% H2O, 5% D2O95% H2O/5% D2O
31.3mM YqbF, U-N15, 13C; 20 mM NH4OAc, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 100% D2O100% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 298 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.1T.D. Goddard, D.G. Knellerdata analysis
NMRPipeLinuz9F. Delaglio, A. Baxprocessing
xplor-NIH2.15.0C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clorerefinement
CNS1.1A. Brunger, G. L .Warrenrefinement
VNMR6.1cVariancollection
RefinementMethod: distance geometry simulated annealing, CNS water refinement
Software ordinal: 1
NMR representativeSelection criteria: lowest total energy
NMR ensembleConformer selection criteria: structures with the lowest bond energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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