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- PDB-2joe: NMR Structure of E. Coli YehR Protein. Northeast Structural Genom... -

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Basic information

Entry
Database: PDB / ID: 2joe
TitleNMR Structure of E. Coli YehR Protein. Northeast Structural Genomics Target ER538.
ComponentsHypothetical lipoprotein yehR
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / six antiparallel beta strands / alpha + beta sandwich / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


YehR-like fold / YehR-like / Protein of unknown function DUF1307 / YehR-like superfamily / Protein of unknown function (DUF1307) / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized lipoprotein YehR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsDing, K. / Ramelot, T.A. / Cort, J.R. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Ding, K. / Ramelot, T.A. / Cort, J.R. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Structure of E. Coli YehR Protein
Authors: Ding, K. / Ramelot, T.A. / Cort, J.R. / Jiang, M. / Xiao, R. / Swapna, G.V.T. / Montelione, G.T. / Kennedy, M.A.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical lipoprotein yehR


Theoretical massNumber of molelcules
Total (without water)15,3881
Polymers15,3881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the lowest NOE and bond energy
RepresentativeModel #1lowest total energy

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Components

#1: Protein Hypothetical lipoprotein yehR


Mass: 15388.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yehR / Production host: Escherichia coli (E. coli) / References: UniProt: P33354

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-15N HSQC
2213D HNCO
2313D HNCA
2413D HN(CO)CA
2513D CBCA(CO)NH
2613D HN(CA)CB
2713D HBHA(CO)NH
2823D HNHA
2913D C(CO)NH
21013D H(CCO)NH
21113D (H)CCH-TOCSY
21232D 1H-13C HSQC
21312D 1H-13C (Arom) HSQC
11412D 1H-15N HSQC
21512D 1H-15N (NH2) HSQC
11623D 1H-15N NOESY
11713D 1H-13C (Aliph) NOESY
11813D 1H-13C (Arom) NOESY
21933D 1H-13C (Aliph) NOESY
22034D 1H-13C NOESY
12122D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] protein, 20 mM NH4OAc, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-5% 13C; U-100% 15N] protein, 20 mM NH4OAc, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-100% 13C; U-100% 15N] protein, 20 mM NH4OAc, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % NaN3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-100% 13C; U-100% 15N]1
20 mMNH4OAc1
100 mMNaCl1
10 mMDTT1
5 mMCaCl21
0.02 %NaN31
1 mMprotein[U-5% 13C; U-100% 15N]2
20 mMNH4OAc2
100 mMNaCl2
10 mMDTT2
5 mMCaCl22
0.02 %NaN32
1 mMprotein[U-100% 13C; U-100% 15N]3
20 mMNH4OAc3
100 mMNaCl3
10 mMDTT3
5 mMCaCl23
0.02 %NaN33
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 5.5 ambient 283 K
2100 5.5 ambient 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
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.1Goddardpeak picking
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AutoStructure2.1.1Huang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelionedata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: distance geometry simulated annealing using NIH xplor, followed by cns water refinement.
NMR constraintsNOE constraints total: 1110 / NOE intraresidue total count: 0 / NOE long range total count: 621 / NOE medium range total count: 314 / NOE sequential total count: 175 / Hydrogen bond constraints total count: 72 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 80 / Protein psi angle constraints total count: 81
NMR representativeSelection criteria: lowest total energy
NMR ensembleConformer selection criteria: structures with the lowest NOE and bond energy
Conformers calculated total number: 30 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.032 Å / Maximum torsion angle constraint violation: 0.5 ° / Maximum upper distance constraint violation: 0.034 Å
NMR ensemble rmsDistance rms dev: 0.002 Å

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