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- PDB-2hjj: Solution NMR structure of protein ykfF from Escherichia coli. Nor... -

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Basic information

Entry
Database: PDB / ID: 2hjj
TitleSolution NMR structure of protein ykfF from Escherichia coli. Northeast Structural Genomics target ER397.
ComponentsHypothetical protein ykfF
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ER397 / Northeast Structural Genomics Consortium (NESG) / Protein Structure Initiative. / PSI-2
Function / homologyykff protein like domains / Protein of unknown function DUF905 / YkfF-like domain superfamily / Bacterial protein of unknown function (DUF905) / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / UPF0401 protein YkfF
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsSwapna, G.V.T. / Aramini, J.M. / Zhao, L. / Cunningham, K. / Janjua, H. / Ma, L.-C. / Xiao, R. / Baran, M.C. / Acton, T.B. / Liu, J. ...Swapna, G.V.T. / Aramini, J.M. / Zhao, L. / Cunningham, K. / Janjua, H. / Ma, L.-C. / Xiao, R. / Baran, M.C. / Acton, T.B. / Liu, J. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of protein ykfF from Escherichia coli. Northeast Structural Genomics target ER397.
Authors: Swapna, G.V.T. / Aramini, J.M. / Zhao, L. / Cunningham, K. / Janjua, H. / Ma, L.-C. / Xiao, R. / Baran, M.C. / Acton, T.B. / Liu, J. / Rost, B. / Montelione, G.T.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ykfF


Theoretical massNumber of molelcules
Total (without water)10,0961
Polymers10,0961
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 ykfF


Mass: 10096.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ykfF / Plasmid: ER397-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: P75677

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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
1323D 13C-separated NOESY
141HNHA
153high resolution CH-HSQC (stereospecific assignment of Val/Leu methyls)
1613D GFT backbone expts
1713D (H)CCH-COSY and (H)CCH-TOCSYs
NMR detailsText: THE STRUCTURE WAS DETERMINED USING GFT AND TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE FROM THE GFT DATA USING AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED ...Text: THE STRUCTURE WAS DETERMINED USING GFT AND TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE FROM THE GFT DATA USING AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 95.3%, SIDE CHAIN, 93.9%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 90.9%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 10 TO 75, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 11-67,72-74: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 85.9%, ADDITIONALLY ALLOWED, 13.8%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.1%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.45/-1.46, ALL, -0.38/-2.25. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 29.98/-3.62. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.956, PRECISION, 0.934, F-MEASURE, 0.945, DP-SCORE, 0.848.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5, 5% D2O / 95% H2O5% D2O / 95% H2O
20.95 mM U-13C,15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5, 100% D2O100% D2O
30.95 mM 5%-13C,U-15N-ER397, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5, 5% D2O / 95% H2O5% D2O / 95% H2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
TopSpin1.3Brukercollection
AutoAssign2.1.1Zimmerman, Moseley, Montelionerefinement
XPLOR-NIH2.11.2Clore et alrefinement
AutoStructure2.1.1Huang & Montelionerefinement
AGNuS2Moseley & Montelioneprocessing
PdbStat4.1Tejero & Montelionedata analysis
PSVS1.3Bhattacharya, Hang, Montelionedata analysis
CNS1.1Brunger et alrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1044 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 72 DIHEDRAL ANGLE CONSTRAINTS, AND 52 HYDROGEN BOND CONSTRAINTS (17.7 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1044 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 72 DIHEDRAL ANGLE CONSTRAINTS, AND 52 HYDROGEN BOND CONSTRAINTS (17.7 CONSTRAINTS PER RESIDUE, 5.3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 10 to 75 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE UNSTRUCTURED N- AND C- TERMINI OF THE PROTEIN WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION.
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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