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- PDB-2k5w: Solution NMR Structure of Putative Lipoprotein from Bacillus cere... -

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Basic information

Entry
Database: PDB / ID: 2k5w
TitleSolution NMR Structure of Putative Lipoprotein from Bacillus cereus Ordered Locus BC_2438. Northeast Structural Genomics Target BcR103A.
ComponentsHypothetical Cytosolic Protein BcR103A
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF1093 / Protein of unknown function DUF1093 / YxeA-like superfamily / Protein of unknown function (DUF1093) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Hypothetical Cytosolic Protein
Function and homology information
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsConover, K.M. / Swapna, G. / Rossi, P. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Conover, K.M. / Swapna, G. / Rossi, P. / Wang, D. / Janjua, H. / Owens, L. / 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 Bacillus cereus Ordered Locus BC_2438. Northeast Structural Genomics Target BcR103A.
Authors: Conover, K.M. / Swapna, G. / Rossi, P. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: Hypothetical Cytosolic Protein BcR103A


Theoretical massNumber of molelcules
Total (without water)13,9211
Polymers13,9211
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 #1lowest energy

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Components

#1: Protein Hypothetical Cytosolic Protein BcR103A


Mass: 13920.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: cereus
Description: Expression Media MJ9 100%N15 5%C13 and MJ9 100%N15 100%C13
Gene: BC_2438 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q813L1

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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-13C NOESY ARO
1413D 1H-13C-15N SIM NOESY
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D CBCA(CO)NH
1913D HNCA
11013D HN(CO)CA
11113D (H)CCH-TOCSY
11213D (H)CCH-COSY
11313D CCH-TOCSY
11422D 1H-15N HSQC
11522D 1H-13C HSQC stereo
1162HETNOE
1173slow exch 1H-15N HSQC
11833D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21.37 mM [5% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-100% 13C; U-100% 15N] BcR103A, 50 uM DSS, 10 mM DTT, 0.02 % sodium azide, 20 mM MES, 5 mM calcium chloride, 100 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMBcR103A[U-100% 13C; U-100% 15N]1
50 uMDSS1
10 mMDTT1
0.02 %sodium azide1
20 mMMES1
5 mMcalcium chloride1
100 mMsodium chloride1
1.37 mMBcR103A[5% 13C; U-100% 15N]2
50 uMDSS2
10 mMDTT2
0.02 %sodium azide2
20 mMMES2
5 mMcalcium chloride2
100 mMsodium chloride2
0.5 mMBcR103A[U-100% 13C; U-100% 15N]3
50 uMDSS3
10 mMDTT3
0.02 %sodium azide3
20 mMMES3
5 mMcalcium chloride3
100 mMsodium chloride3
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
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
TopSpin2.1Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionevalidation
PdbStat5.1Tejero R.; Montelione GTvalidation
MOLMOL2k2Koradi, Billeter and Wuthrichvisualization
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thovalidation
MolProbityRichardsonvalidation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 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 ...Details: 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 85.1%, SIDECHAIN 78.2%, AROMATIC (SC) 76.7%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1446 NOE, 137 DIHE. MAX NOE VIOLATION: 0.36 A (1MODEL); MAX DIHE VIOLATION: 6.6 DEG. 16 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 9-11, 13-18,23-51, 67-75, 87-107 FOR [S(PHI)+S(PSI)] > 1.8. SECONDARY STRUCTURE - BETA STRANDS: (13-17, 24-27, 30-33, 35-41, 46-51, 67-72, 87-93). RMSD 1.0 BACKBONE, 1.3 ALL HEAVY ATOMS. RAMA. DISTRIBUTION: 95.7/4.2/0.1/0.0. PROCHECK (PSI-PHI): -0.31/-0.90(RAW/Z), PROCHECK (ALL): -0.16/-0.95 (RAW/Z), MOLPROBITY CLASH: 15.17/-1.08 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.99, PRECISION: 0.90, F-MEASURE: 0.94 DP-SCORE: 0.803.
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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