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- PDB-2mu4: Structure of F. tularensis Virulence Determinant -

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Basic information

Entry
Database: PDB / ID: 2mu4
TitleStructure of F. tularensis Virulence Determinant
Componentsflpp3Sol_2
KeywordsMEMBRANE PROTEIN / lipoprotein
Function / homologyLipoprotein Flpp3-like / Protein of unknown function (DUF3568) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Hypothetical lipoprotein
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis SCHU S4 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsZook, J.J.D.Z. / Mo, G.G.M. / Craciunescu, F.F.C. / Sisco, N.N.S. / Hansen, D.D.H. / Baravati, B.B.B. / Van Horn, W.W.V.H. / Cherry, B.B.C. / Fromme, P.P.F.
CitationJournal: Structure / Year: 2015
Title: NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins.
Authors: Zook, J. / Mo, G. / Sisco, N.J. / Craciunescu, F.M. / Hansen, D.T. / Baravati, B. / Cherry, B.R. / Sykes, K. / Wachter, R. / Van Horn, W.D. / Fromme, P.
History
DepositionSep 3, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: flpp3Sol_2


Theoretical massNumber of molelcules
Total (without water)13,2751
Polymers13,2751
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein flpp3Sol_2 / lipoprotein


Mass: 13275.465 Da / Num. of mol.: 1 / Fragment: UNP residues 26-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis SCHU S4 (bacteria)
Strain: Schu S4
Description: Lemo mechanism not selected for with chloramphenicol
Gene: FTT1416c, FTT_1416c / Cell line (production host): Lemo21 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q5NF33

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC/HMQC
1223D HNCO
132HN(CA)CO (HN(CA)CO)
1423D HNCA
1523D HN(CA)CB
1623D CBCA(CO)NH
1723D 1H-15N NOESY
182C(CO)NH (C coNH.relayed)
1923D (H)CCH-TOCSY
11023D H(CCO)NH
11123D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-99% 13C; U-99% 15N] flpp3Sol_2, 95 % H2O, 5 % D2O, 90 mM Sodium Chloride, 20 mM Sodium Phosphate, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-99% 13C; U-99% 15N] flpp3Sol_2, 95 % H2O, 5 % D2O, 90 mM Sodium Chloride, 20 mM Sodium Phosphate, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMflpp3Sol_2-1[U-99% 13C; U-99% 15N]1
95 %H2O-21
5 %D2O-31
90 mMSodium Chloride-41
20 mMSodium Phosphate-51
0.8 mMflpp3Sol_2-6[U-99% 13C; U-99% 15N]2
95 %H2O-72
5 %D2O-82
90 mMSodium Chloride-92
20 mMSodium Phosphate-102
Sample conditionsIonic strength: 0.11 / pH: 6.8 / Pressure: 1.000 atm / Temperature: 298.150 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8502

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4CCPNspectrum analysis
NMRDrawanyDelagliospectrum display
NMRPipeanyDelagliospectrum processing
CNSrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Water bath molecular dynamics.
NMR constraintsNOE constraints total: 1945 / NOE intraresidue total count: 306 / NOE long range total count: 639 / NOE medium range total count: 397 / NOE sequential total count: 603 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 96 / Protein psi angle constraints total count: 96
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.54433 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 8.014 ° / Maximum upper distance constraint violation: 0.235 Å
NMR ensemble rmsDistance rms dev: 0.01095 Å / Distance rms dev error: 0.01083 Å

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