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- PDB-2krt: Solution NMR Structure of a Conserved Hypothetical Membrane Lipop... -

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Basic information

Entry
Database: PDB / ID: 2krt
TitleSolution NMR Structure of a Conserved Hypothetical Membrane Lipoprotein Obtained from Ureaplasma parvum: Northeast Structural Genomics Consortium Target UuR17A (139-239)
ComponentsConserved hypothetical membrane lipoprotein
KeywordsLIPID BINDING PROTEIN / Lipoprotein / NESG / UuR17A / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Nuclear Transport Factor 2; Chain: A, - #270 / Lipoprotein-associated domain / Lipoprotein associated domain / Uncharacterised protein family MG067 / Mycoplasma peptidase DUF31 / Mycoplasma peptidase (DUF31) / Nuclear Transport Factor 2; Chain: A, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Membrane-associated lipoprotein
Similarity search - Component
Biological speciesUreaplasma parvum (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMani, R. / Swapna, G. / Janjua, H. / Ciccosanti, C. / Huang, Y. / Patel, D. / Xiao, R. / Acton, T. / Everett, J. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Solution Structure of a Conserved Hypothetical Membrane Lipoprotein obtained from Ureaplasma parvum : Northeast Structural Genomics Consortium Target UuR17A (139-239)
Authors: Mani, R. / Swapna, G. / Janjua, H. / Ciccosanti, C. / Huang, Y. / Patel, D. / Xiao, R. / Acton, T. / Everett, J. / Montelione, G.T.
History
DepositionDec 22, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 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_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved hypothetical membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)14,3561
Polymers14,3561
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 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Conserved hypothetical membrane lipoprotein


Mass: 14356.188 Da / Num. of mol.: 1 / Fragment: residues 128-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureaplasma parvum (bacteria) / Gene: UU045 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9PRA0

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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
1313D 1H-15N/13C simultaneous NOESY
1413D 1H-13C arom NOESY
1522D 1H-15N HSQC
1622D 1H-13C HSQC
1723D CBCA(CO)NH
1823D HBHA(CO)NH
1923D HNCO
11023D HNCA
11123D HN(CA)CB
1122(4,3)D GFT-CBCACACONHN
1132(4,3)D GFT-HNNCABCA
11423D CCH-TOCSY
11523D (H)CCH-TOCSY
11623D CC(CO)NH TOCSY
11733D HNHA
1183Het NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.91 mM [U-100% 13C; U-100% 15N] UuR17A, Lipoprotein, 95% H2O/5% D2O95% H2O/5% D2O
20.91 mM [U-100% 13C; U-100% 15N] UuR17A, Lipoprotein, 95% H2O/5% D2O95% H2O/5% D2O
30.7 mM [U-10% 13C; U-99% 15N] UuR17A, Lipoprotein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.91 mMUuR17A, Lipoprotein[U-100% 13C; U-100% 15N]1
0.91 mMUuR17A, Lipoprotein[U-100% 13C; U-100% 15N]2
0.7 mMUuR17A, Lipoprotein[U-10% 13C; U-99% 15N]3
Sample conditionsIonic strength: 5mM CaCl2, 10mM Nacl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was obtained using triple resonance NMR spectroscopy. GFT_NMR experiments were used for backbone resosnance assignments and conventional 3D TOCSY experiments were used for ...Details: The structure was obtained using triple resonance NMR spectroscopy. GFT_NMR experiments were used for backbone resosnance assignments and conventional 3D TOCSY experiments were used for sidechain assignments. Automated NOESY assignments were made using AUTOSTRUCTURE and CYANA-3.0 software. Dihedral angle constraints were obtained using TALOS. The structure calculation was done excluding the 8-residue C-terminal tag (LEHHHHHH). Final structure quality factor excluding C-terminal tag: as determined by PSVS-v1-4: Ordered residues are defined as 5-71, 74-114. (a) RMSD (ordered residue) all backbone atoms - 0.7A, heacyatoms - 1.1A. (b) Ramachandran statistics for ordered residues: Most favored region: 85.1%, additionally favored: 14.6%, Generously allowed: 0.4%. (c) Procheck scores for ordered residues (RAW/Z): Phi/psi - -0.42/-1.34, all - -0.40/-2.37. (d) MolProbity clashscores (RAW/Z) - 21.86/-2.23. (e) RPF scores for the goodness fit to NOESY data: Recall - 0.917, Precision - 0.928, F-measure 0.923 and final dp-score - 0.755.
NMR constraintsNOE constraints total: 2045 / NOE intraresidue total count: 388 / NOE long range total count: 625 / NOE medium range total count: 440 / NOE sequential total count: 592 / Protein phi angle constraints total count: 64 / Protein psi angle constraints total count: 64
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.1 Å / Maximum upper distance constraint violation: 0.5 Å / Torsion angle constraint violation method: PSVS software
NMR ensemble rmsDistance rms dev: 0.01 Å

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