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- PDB-2hh8: Solution NMR structure of the ydfO protein from Escherichia coli.... -

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Basic information

Entry
Database: PDB / ID: 2hh8
TitleSolution NMR structure of the ydfO protein from Escherichia coli. Northeast Structural Genomics target ER251.
ComponentsHypothetical protein ydfO
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ER251 / AutoStructure / NESG / PSI-2 / Northeast Structural Genomics Consortium / Protein Structure Initiative
Function / homologyYdfO-like fold / YdfO-like / Uncharacterised protein DUF1398 / YdfO-like superfamily / Protein of unknown function (DUF1398) / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein YdfO
Function and homology information
Biological speciesEscherichia coli (E. coli)
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 1885 constraints, 788 long range, 142 dihedral constraints, 114 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 ydfO protein from Escherichia coli. Northeast Structural Genomics target ER251.
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 28, 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: Hypothetical protein ydfO


Theoretical massNumber of molelcules
Total (without water)18,1471
Polymers18,1471
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 Hypothetical protein ydfO


Mass: 18146.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Escherichia coli O6 / Gene: ydfO / Plasmid: ER251_21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: P76156

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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
152C13 HSQC noct Stereospecific VL Me assign.
162Het-NOE, T1/T1rho
1733D 13C-separated NOESY
NMR detailsText: Structure determined by triple resonance NMR spectroscopy. Monomer under NMR conditions. TC = 9.1 +/-0.5 ns (1D T1/T1rho +/- FIT STD). Coordinates reported from residue 7 to 133 based on order ...Text: Structure determined by triple resonance NMR spectroscopy. Monomer under NMR conditions. TC = 9.1 +/-0.5 ns (1D T1/T1rho +/- FIT STD). Coordinates reported from residue 7 to 133 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 96.7%, sidechain 83.7%, aromatic (sc) 79.8%, VL methyl stereospecific 100%, unambiguos sidechain NH2 88.9%. Structure quality factor PSVS 1.3: ordered residues ranges alpha helix (8-22, 26-35, 76-88, 93-102), b-strand (39-43, 48-52, 58-62, 107-111, 116-120, 126-131) [S(phi)+S(psi)]>1.8. RMSD 0.5 bb, 1.1 all heavy atoms. Rama: 87.4% most fav, 12.5% addtl. all., 0.0 gen. all.,0.0% disall. Procheck (psi-phi): -0.17/-0.35 (raw/Z), Procheck (all): -0.15/-0.89 (raw/Z), MolProbity Clash: 24.43/-2.67 (raw/Z) . RPF scores all assigned residues (fit of noesy peaklists to structure): Recall: 0.965, Precision: 0.919, F-measure: 0.942, DP-score: 0.817. L139F cloning mutation of E. coli ydfO gene present.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.69mM U-13C,15N ER251, 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM Ammonium acetate, 5% D2O5% D2O, 95% H2O
20.74mM 5%-13C,U-15N ER251 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM Ammonium acetate, 5% D2O5% D2O, 95% H2O
30.69mM U-13C,15N ER251, 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM Ammonium acetate, 5% D2O99.9% D2O
Sample conditionsIonic strength: 0.1 M NaCl / pH: 4.5 / 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Varian INOVAVarianINOVA7503
Varian INOVAVarianINOVA6004

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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
CNS1.1Brungerrefinement
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 1885 constraints, 788 long range, 142 dihedral constraints, 114 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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