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- PDB-2juz: Solution NMR structure of HI0947 from Haemophilus influenzae, Nor... -

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Basic information

Entry
Database: PDB / ID: 2juz
TitleSolution NMR structure of HI0947 from Haemophilus influenzae, Northeast Structural Genomics Consortium Target IR123
ComponentsUPF0352 protein HI0840
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / homodimer / helix / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyUncharacterised protein family UPF0352 / YejL-like superfamily / Protein of unknown function (DUF1414) / YejL-like / YejL-like / Orthogonal Bundle / Mainly Alpha / UPF0352 protein HI_0840
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsDing, K. / Ramelot, T.A. / Cort, J.R. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. ...Ding, K. / Ramelot, T.A. / Cort, J.R. / Wang, D. / Nwosu, C. / Owens, 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: Solution NMR Structure of HI0947 from Haemophilus influenzae.
Authors: Ding, K. / Ramelot, T.A. / Cort, J.R. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionSep 9, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0352 protein HI0840
B: UPF0352 protein HI0840


Theoretical massNumber of molelcules
Total (without water)17,5242
Polymers17,5242
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 / 25structures with the lowest bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein UPF0352 protein HI0840


Mass: 8761.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: DSM 11121, KW20, Rd / Gene: HI0840 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P44897

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C Arom HSQC
1413D HNCO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HNHA
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D 1H-13C Arom NOESY
11324D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.66 mM [U-100% 13C; U-100% 15N] protein, 5 mM CaCl2, 100 mM NaCl, 20 mM NH4OAc, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
20.66 mM [U-100% 13C; U-100% 15N] protein, 5 mM CaCl2, 100 mM NaCl, 20 mM NH4OAc, 10 mM DTT, 0.02 % NaN3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.66 mMprotein[U-100% 13C; U-100% 15N]1
5 mMCaCl21
100 mMNaCl1
20 mMNH4OAc1
10 mMDTT1
0.02 %NaN31
0.66 mMprotein[U-100% 13C; U-100% 15N]2
5 mMCaCl22
100 mMNaCl2
20 mMNH4OAc2
10 mMDTT2
0.02 %NaN32
Sample conditionsIonic strength: 100 / pH: 5.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
AutoStructure2.1.1Huang, Tejero, Powers and Montelionedata analysis
Sparky3.1Goddardpeak picking
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: DGSA using xplor NIH and then followed by CNS water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest bond energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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