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- PDB-2jxp: Solution NMR structure of uncharacterized lipoprotein B from Nitr... -

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Basic information

Entry
Database: PDB / ID: 2jxp
TitleSolution NMR structure of uncharacterized lipoprotein B from Nitrosomonas europaea. Northeast Structural Genomics target NeR45A
ComponentsPutative lipoprotein B
KeywordsLIPOPROTEIN / Uncharacterized Lipoprotein B / Northeast Structural Genomics Consortium / NESG / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / lipopolysaccharide binding
Similarity search - Function
Lipoprotein like domain / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
LPS-assembly lipoprotein LptE
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRossi, P. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of uncharacterized lipoprotein B from Nitrosomonas europaea.
Authors: Rossi, P. / Xiao, R. / Acton, T.B. / Montelione, G.T.
History
DepositionNov 27, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Putative lipoprotein B


Theoretical massNumber of molelcules
Total (without water)17,6141
Polymers17,6141
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative lipoprotein B


Mass: 17614.246 Da / Num. of mol.: 1 / Fragment: Residues 20-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria)
Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: rlpB, NE1138 / Plasmid: NeR45A-21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q82VF2

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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 CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HN(CO)CA
1713D HBHA(CO)NH
1813D SIMULTANEOUS 15N-13C NOESY
1923D 1H-13C NOESY
11013D (H)CCH-COSY
11113D (H)CCH-TOCSY
11213D CCH-TOCSY
11332D 1H-13C HSQC
11413D HNCO
11513D HN(CA)CO
NMR detailsText: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION ...Text: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA2.1. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 98.9%, SIDECHAIN 86.6%, AROMATIC (SC) 78.4%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2279 NOE. MAX NOE VIOLATION 0.46 A (1 MODEL). 22 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES - ALPHA HELICES: (26-38, 114-117, 120-143), BETA STRANDS: (42-44, 16-20, 52-65, 76-89, 100-108, 94-96, 68-69, 73-74) FOR [S(PHI)+S(PSI)] > 1.8. RMSD 0.7 BB, 1.3 ALL HEAVY ATOMS. RAMA. DISTRIBUTION: 90.4/9.5/0.1/0.0. PROCHECK (PSI-PHI): -0.34/-1.02 (RAW/Z), PROCHECK (ALL): -0.35/-2.07 (RAW/Z), MOLPROBITY CLASH: 20.44/-1.98 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.868, PRECISION: 0.871, F-MEASURE: 0.869, DP-SCORE: 0.706.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.86 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 100% D2O100% D2O
31.3 mM lipoprotein B, 20 mM MES, 5 mM calcium chloride, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMlipoprotein B1
20 mMMES1
5 mMcalcium chloride1
100 mMDTT1
100 mMsodium chloride1
0.02 %sodium azide1
0.86 mMlipoprotein B2
20 mMMES2
5 mMcalcium chloride2
100 mMDTT2
100 mMsodium chloride2
0.02 %sodium azide2
1.3 mMlipoprotein B3
20 mMMES3
5 mMcalcium chloride3
100 mMDTT3
100 mMsodium chloride3
0.02 %sodium azide3
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssign2.4Zimmerman, Moseley, Kulikowski and Montelionebackbone chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionevalidation
Sparky3.112Goddarddata analysis
TopSpin1.3Bruker Biospincollection
MOLMOL2.2Koradi, Billeter and Wuthrichvisualization
RPF2.1.1Huang, Powers and Montelionevalidation
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss et al.validation
MolProbityRichardsonvalidation
XEASYBartels et al.data analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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