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- PDB-2fj6: Solution NMR structure of the UPF0346 protein yozE from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 2fj6
TitleSolution NMR structure of the UPF0346 protein yozE from Bacillus subtilis. Northeast Structural Genomics target SR391.
ComponentsHypothetical UPF0346 protein yozE
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR391 / AutoStructure / Northeast Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function UPF0346 / YozE SAM-like / YozE SAM-like domain / YozE SAM-like superfamily / YozE SAM-like fold / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / UPF0346 protein YozE
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / Noesy assignments using AutoStructure, dyana, xplor for simulated annealing with a total of 1096 NOE distances. An average of 16.6 constraints, restrained res, 3.7 of which long range. 208 dihedral angle constraints, 42 h-bond constraints.
AuthorsRossi, P. / Acton, T.B. / Cunningham, K.E. / Ma, L.C. / Shetty, K. / Swapna, G.V.T. / Xiao, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the UPF0346 protein yozE from Bacillus subtilis. Northeast Structural Genomics target SR391.
Authors: Rossi, P. / Acton, T.B. / Cunningham, K.E. / Ma, L.C. / Shetty, K. / Swapna, G.V.T. / Xiao, R. / Montelione, G.T.
History
DepositionDec 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 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_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 UPF0346 protein yozE


Theoretical massNumber of molelcules
Total (without water)9,9961
Polymers9,9961
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)10 / 56structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical UPF0346 protein yozE


Mass: 9995.864 Da / Num. of mol.: 1 / Fragment: protein yozE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yozE / Plasmid: SR391-21.1-ss / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: O31864

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
132HNCA-J
142HiRes-CH HSQC for stereospec. VL Methyl assign.
151HN(CA)CB, HN(CO)CACB, HNCO,HNCA
161CC(CO)NH TOCSY, (H)CCH-COSY
171(HA)CA(CO)NH single transfer
NMR detailsText: Automated backbone assignement using AutoAssign, manual sidechain assignment. Completeness: 95.3% BB, 88.2% SC, and 100% stereospecific Methyl assignments. Dihe. constr. determined with Talos ...Text: Automated backbone assignement using AutoAssign, manual sidechain assignment. Completeness: 95.3% BB, 88.2% SC, and 100% stereospecific Methyl assignments. Dihe. constr. determined with Talos and Hyper. RPF scores for NOE data consistency: Recall=0.932, Precision=0.874, F-measure=0.902 final DP score=0.738. RMSD ordered residues: 0.5 all BB, 1.0 all heavy atoms. Raw Procheck: psi-phi=0.1, all=-0.2, MolProbity 16.16. N-term tag included.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM U-13C,15N SR391, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN35% D2O, 95% H2O
21.35mM 5%-13C,U-15N SR391, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN35% D2O, 95% H2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 5.5 / Pressure: atmospheric atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVarian Inc.collection
xplor-nih2.0.6Clore et. al.refinement
NMRPipe2.5Delaglio et. al.processing
Sparky2.11Goddard, Knellerdata analysis
AutoStructure2.1.1Huang, Montelionestructure solution
AutoAssign1.17Zimmerman, Moseley, Montelionedata analysis
RefinementMethod: Noesy assignments using AutoStructure, dyana, xplor for simulated annealing with a total of 1096 NOE distances. An average of 16.6 constraints, restrained res, 3.7 of which long range. 208 ...Method: Noesy assignments using AutoStructure, dyana, xplor for simulated annealing with a total of 1096 NOE distances. An average of 16.6 constraints, restrained res, 3.7 of which long range. 208 dihedral angle constraints, 42 h-bond constraints.
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 56 / Conformers submitted total number: 10

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