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- PDB-2k57: Solution NMR Structure of Putative Lipoprotein from Pseudomonas s... -

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Basic information

Entry
Database: PDB / ID: 2k57
TitleSolution NMR Structure of Putative Lipoprotein from Pseudomonas syringae Gene Locus PSPTO2350. Northeast Structural Genomics Target PsR76A.
ComponentsPutative Lipoprotein
Keywordsstructural genomics / unknown function / putative lipoprotein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Lipoprotein
Function / homology
Function and homology information


Protein of unknown function DUF903 / : / Bacterial protein of unknown function (DUF903) / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Mainly Beta
Similarity search - Domain/homology
Lipoprotein, putative
Similarity search - Component
Biological speciesPseudomonas syringae pv. phaseolicola 1448A (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsputative lipoprotein truncated lipo-box
AuthorsHang, D. / Aramini, J.A. / Rossi, P. / Wang, D. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Hang, D. / Aramini, J.A. / Rossi, P. / Wang, D. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Putative Lipoprotein from Pseudomonas syringae Gene Locus PSPTO2350. Northeast Structural Genomics Target PsR76A.
Authors: Rossi, P. / Aramini, J.A. / Hang, D. / Xiao, R. / Acton, T.B. / Montelione, G.T.
History
DepositionJun 25, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,1691
Polymers7,1691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1

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Components

#1: Protein Putative Lipoprotein


Mass: 7168.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola 1448A (bacteria)
Species: syringae / Gene: PSPPH_2109 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q48JU9

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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 HSQC CT ARO
1413D HNCO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HN(CA)CO
1813D 1H-13C -15N SIM NOESY
191N15-T1
1101N15- T2(CPMG)
11113J NHHA
11213D (H)CCH-COSY
11313D (H)CCH-TOCSY
11413D CCH- TOCSY
11513D CC(CO)NH-TOCSY
11612D 1H
117115N HETNOE
11812D 1H-13C HSQC STEREO
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 BACKBONE 98.2%, SIDECHAIN 91.0%, AROMATIC (SC) 55.6%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1027 NOE, 133 DIHE. MAX NOE VIOLATION: 0.14 A (1MODEL); MAX DIHE VIOLATION: 3.1 DEG. 2 TOTAL CLOSE ORDERED RESIDUES RANGES: 1-71 FOR [S(PHI)+S(PSI)] > 1.8. SECONDARY STRUCTURE - BETA STRANDS: (8-17, 20-26, 29-33, 51- 60, 65-70). RMSD 0.4 BACKBONE, 0.7 ALL HEAVY ATOMS. RAMA. CLASH: 11.98/-0.53 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES PRECISION: 0.92, F-MEASURE: 0.95, DP-SCORE: 0.799.

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Sample preparation

DetailsContents: 1.07 MM [U-100% 13C 15N] PSR76A, 50 UM DSS, 10 MM DTT, 100 MM SODIUM CHLORIDE, 0.02 % SODIUM AZIDE, 20 MM MES, 5 MM CALCIUM CHLORIDE, 90% H2O/10% D2O; 1.07 MM [5% 13C; U-100% 15N] PSR76A, ...Contents: 1.07 MM [U-100% 13C 15N] PSR76A, 50 UM DSS, 10 MM DTT, 100 MM SODIUM CHLORIDE, 0.02 % SODIUM AZIDE, 20 MM MES, 5 MM CALCIUM CHLORIDE, 90% H2O/10% D2O; 1.07 MM [5% 13C; U-100% 15N] PSR76A, 50 UM DSS, 10 MM DTT, 100 MM SODIUM CHLORIDE, 0.02 % SODIUM AZIDE, 20 MM MES, 5 MM CALCIUM CHLORIDE, 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.07 mMPsR76A[U-100% 13C; U-100% 15N]1
50 uMDSS1
10 mMDTT1
100 mMsodium chloride1
0.02 %sodium azide1
20 mMMES1
5 mMcalcium chloride1
1.07 mMPsR76A[5% 13C; U-100% 15N]2
50 uMDSS2
10 mMDTT2
100 mMsodium chloride2
0.02 %sodium azide2
20 mMMES2
5 mMcalcium chloride2
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER, ADAMS, CLORE, GROS, NILGESrefinement
CYANA2.1structure solution
AutoAssign2.4.0structure solution
NMRPipestructure solution
TopSpin2.1structure solution
Sparky3.113structure solution
TALOSstructure solution
RPF(AUTOSTRUCTURE)2.2.1structure solution
MOLMOLstructure solution
PSVSstructure solution
PdbStat5structure solution
MolProbitystructure solution
PROCHECKstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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