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- PDB-2b3w: NMR structure of the E.coli protein YbiA, Northeast Structural Ge... -

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Basic information

Entry
Database: PDB / ID: 2b3w
TitleNMR structure of the E.coli protein YbiA, Northeast Structural Genomics target ET24.
ComponentsHypothetical protein ybiA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ET24 / NESG / YbiA / COG 3236 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


nucleobase-containing small molecule catabolic process / hydrolase activity, hydrolyzing N-glycosyl compounds / carbohydrate derivative metabolic process / riboflavin biosynthetic process / bacterial-type flagellum-dependent swarming motility / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
Similarity search - Function
YbiA-like / NADAR / YbiA-like superfamily / NADAR domain / Tetracycline Repressor; domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry simulated annealing cns water refinement
AuthorsRamelot, T.A. / Cort, J.R. / Xiao, R. / Shih, L.Y. / Acton, T.B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR structure of the E.coli protein YbiA, Northeast Structural Genomics target ET24.
Authors: Ramelot, T.A. / Cort, J.R. / Xiao, R. / Shih, L.Y. / Acton, T.B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionSep 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: 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 22, 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 ybiA


Theoretical massNumber of molelcules
Total (without water)19,7721
Polymers19,7721
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 / -
RepresentativeModel #1closest to the average

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Components

#1: Protein Hypothetical protein ybiA


Mass: 19772.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ybiA / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Lamda DE3) PMGK / References: UniProt: P30176

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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
1324D 13C-separated NOESY
143HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM YbiA, U-15N, 13C; 20 mM MES, 100mM NaCl, 10 mM DTT, 5mM CaCl2, 0.02% NaN3; 95% H2O, 5% D2O95% H2O/5% D2O
21mM YbiA, U-15N, 13C; 20 mM MES, 100mM NaCl, 10 mM DTT, 5mM CaCl2, 0.02% NaN3; 100 % D2O100% D2O
31mM YbiA, U-15N, 5%-13C; 20 mM MES, 100mM NaCl, 10 mM DTT, 5mM CaCl2, 0.02% NaN3; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / 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 INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.1T.D. Goddard, D.G. Knellerdata analysis
NMRPipeLinux9F. Delaglio, A. Baxprocessing
AutoStructure2.1.1Y.J. Huang, G.T. Montelionedata analysis
X-PLORxplor-nih-2.10C.D Schwieters, J.J.Kuszewski, N. Tjandra, G.M. Clorestructure solution
CNS1.1A. Brunger, G.L. Warrenrefinement
VNMR6.1cVariancollection
RefinementMethod: distance geometry simulated annealing cns water refinement
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1598 RESTRAINTS. 1298 are NOE-DERIVED; SEQUENTIAL [(I-J)=1] = 1; MEDIUM RANGE [10.1 ANG = 0; AVERAGE R.M.S. DISTANCE VIOLATION = 0.002 ANG. AVERAGE ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1598 RESTRAINTS. 1298 are NOE-DERIVED; SEQUENTIAL [(I-J)=1] = 1; MEDIUM RANGE [1<(I-J)<5] = 498; LONG RANGE [(I-J)>=5] = 632; HYDROGEN BOND RESTRAINTS = 94 (2 PER H-BOND); NUMBER OF NOE RESTRAINTS PER RESIDUE = 8.1 (RESIDES 2-164); DIHEDRAL-ANGLE RESTRAINTS = 206 (103 PHI, 103 PSI); TOTAL NUMBER OF RESTRAINTS PER RESIDUE = 10.0 (RESIDES 2-164); NUMBER OF LONG RANGE RESTRAINTS PER RESIDUE = 4.0; NUMBER OF STRUCTURES COMPUTED = 25; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.1 ANG = 0; AVERAGE R.M.S. DISTANCE VIOLATION = 0.002 ANG. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0 DEG = 5.1; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 10; AVERAGE R.M.S. ANGLE VIOLATION = 0.06 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 15-162) = 0.87 ANG; ALL HEAVY ATOMS = 1.29 ANG; PROCHECK (RESIDUES 15-162): MOST FAVORED REGIONS = 87%; ADDITIONAL ALLOWED REGIONS = 10%; GENEROUSLY ALLOWED REGIONS = 2%; DISALLOWED REGIONS = 1%.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformers submitted total number: 20

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