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- PDB-2le1: Solution NMR Structure of Tfu_2981 from Thermobifida fusca, North... -

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Basic information

Entry
Database: PDB / ID: 2le1
TitleSolution NMR Structure of Tfu_2981 from Thermobifida fusca, Northeast Structural Genomics Consortium Target TfR85A
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homologyPolyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / SRPBCC family protein
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPulavarti, S.V.S.R.K. / Eletsky, A. / Mills, J.L. / Sukumaran, D.K. / Wang, D. / Ciccosanti, C. / Hamilton, K. / Rost, B. / Acton, T.B. / Xiao, R. ...Pulavarti, S.V.S.R.K. / Eletsky, A. / Mills, J.L. / Sukumaran, D.K. / Wang, D. / Ciccosanti, C. / Hamilton, K. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Tfu_2981 from Thermobifida fusca, Northeast Structural Genomics Consortium Target TfR85A
Authors: Pulavarti, S.V.S.R.K. / Eletsky, A. / Mills, J.L. / Sukumaran, D.K. / Wang, D. / Ciccosanti, C. / Hamilton, K. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. ...Authors: Pulavarti, S.V.S.R.K. / Eletsky, A. / Mills, J.L. / Sukumaran, D.K. / Wang, D. / Ciccosanti, C. / Hamilton, K. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 3, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Feb 29, 2012Group: Database references / Structure summary
Revision 1.4Aug 15, 2012Group: Structure summary
Revision 1.5Jun 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 1.6May 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,8811
Polymers16,8811
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 Uncharacterized protein


Mass: 16880.957 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_2981 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q47KK8

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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 CT-HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1713D HN(CA)CO
1813D (H)CCH-TOCSY
191(4,3)D GFT (H)CCH-COSY-aliphatic
1101(4,3)D GFT (H)CCH-COSY-aromatic
11112D 1H-13C CT-HSQC aromatic
11242D 1H-13C CT-HSQC methyl
11342D J-modulation 1H-15N HSQC
11422D J-modulation 1H-15N HSQC
11532D J-modulation 1H-15N HSQC
11612D 1H-15N LR-HSQC for Histidine
11713D HBHA(CO)NH
11812D (HB)CB(CGCDCE)HDHE

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] TfR85A, 20 mM MES, 100 mM sodium chloride, 10 mM DTT, 50 uM DSS, 5 mM calcium chloride, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.338 mM [U-5% 13C; U-100% 15N] TfR85A, 20 mM MES, 100 mM sodium chloride, 10 mM DTT, 50 uM DSS, 5 mM calcium chloride, 0.02 % sodium azide, 12.5 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
31.338 mM [U-5% 13C; U-100% 15N] TfR85A, 20 mM MES, 100 mM sodium chloride, 10 mM DTT, 50 uM DSS, 5 mM calcium chloride, 0.02 % sodium azide, 4 % PEG, 90% H2O/10% D2O90% H2O/10% D2O
41.338 mM [U-5% 13C; U-100% 15N] TfR85A, 20 mM MES, 100 mM sodium chloride, 10 mM DTT, 50 uM DSS, 5 mM calcium chloride, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMTfR85A-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
10 mMDTT-41
50 uMDSS-51
5 mMcalcium chloride-61
0.02 %sodium azide-71
1.338 mMTfR85A-8[U-5% 13C; U-100% 15N]2
20 mMMES-92
100 mMsodium chloride-102
10 mMDTT-112
50 uMDSS-122
5 mMcalcium chloride-132
0.02 %sodium azide-142
12.5 mg/mLPf1 phage-152
1.338 mMTfR85A-16[U-5% 13C; U-100% 15N]3
20 mMMES-173
100 mMsodium chloride-183
10 mMDTT-193
50 uMDSS-203
5 mMcalcium chloride-213
0.02 %sodium azide-223
4 %PEG-233
1.338 mMTfR85A-24[U-5% 13C; U-100% 15N]4
20 mMMES-254
100 mMsodium chloride-264
10 mMDTT-274
50 uMDSS-284
5 mMcalcium chloride-294
0.02 %sodium azide-304
Sample conditionsIonic strength: 0.11 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA7503
Varian INOVAVarianINOVA6004
Varian INOVAVarianINOVA5005

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement, geometry optimization, solution structure
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis,chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PROSA6.4Guntertprocessing
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
PSVSBhattacharya and Montelionestructure analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
CARA1.8.4Keller and Wuthrichdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by CYANA and AUTOSTRUCTURE in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints. Consensus peak assignments generated from ...Details: Structure determination was performed by CYANA and AUTOSTRUCTURE in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints. Consensus peak assignments generated from these parallel runs were selected and used for further refinement with CYANA, the RDC constraints were added at later stages. A total of 20 conformers out of 100 conformers with the lowest target function were selected for refinement with CNS using CNS water bath refinement.
NMR constraintsNOE constraints total: 3877 / NOE intraresidue total count: 415 / NOE long range total count: 1678 / NOE medium range total count: 825 / NOE sequential total count: 959 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 70 / Protein psi angle constraints total count: 70
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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