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- PDB-2h7a: NMR Structure of the Conserved Protein YcgL from Escherichia coli... -

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Basic information

Entry
Database: PDB / ID: 2h7a
TitleNMR Structure of the Conserved Protein YcgL from Escherichia coli representing the DUF709 Family Reveals a Novel a/b/a Sandwich Fold
ComponentsHypothetical protein ycgLHypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Mixed ALPHA/BETA/ALPHA Sandwich Structure / 3-layer (alpha/beta/alpha) sandwich / beta-Sheet Layer Antiparallel 3124 topology / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


YcgL domain / YcgL domain / YcgL-like superfamily / YcgL domain / YcgL domain profile. / NE1680-like fold / Roll / Alpha Beta
Similarity search - Domain/homology
Protein YcgL / Protein YcgL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMinailiuc, O.M. / Vavelyuk, O. / Ekiel, I. / Hung, M.-Ni. / Cygler, M. / Gandhi, S. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Proteins / Year: 2007
Title: NMR structure of YcgL, a conserved protein from Escherichia coli representing the DUF709 family, with a novel alpha/beta/alpha sandwich fold.
Authors: Minailiuc, O.M. / Vavelyuk, O. / Gandhi, S. / Hung, M.N. / Cygler, M. / Ekiel, I.
History
DepositionJun 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: 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 ycgL


Theoretical massNumber of molelcules
Total (without water)12,5781
Polymers12,5781
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 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical protein ycgL / Hypothesis


Mass: 12577.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: ycgL / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q2LD68, UniProt: P0AB44*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1313D 13C-separated NOESY
1412D TOCSY
151HNHA
161HN(CA)CB
171CBCA(CO)NH
181HN(CA)CO
191HNHA
1101HBHA(CO)NH
11113D (H)CCH-TOCSY
11211H-15N TOCSY-HMQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDARD HOMONUCLEAR AND HETERONUCLEAR NMR EXPERIMENTS

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Sample preparation

DetailsContents: 50mM phosphate buffer, pH 6.8, 150mM NaCl, 15mM DTT, 0.02% (w/v) sodium azide, 10% D2O, 90% H2O
Solvent system: 10% D2O, 90% H2O
Sample conditionsIonic strength: 150mM NaCl / pH: 6.8 / Pressure: AMBIENT / Temperature: 308 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
Bruker AVANCEBrukerAVANCE5001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRcollection
NMRPipeFrank Delaglioprocessing
CARA135Rochus Kellerdata analysis
XEASYdata analysis
CYANA2.1Peter Guntertstructure solution
XPLOR-NIH2112refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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