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- PDB-2lf0: Solution structure of sf3636, a two-domain unknown function prote... -

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Basic information

Entry
Database: PDB / ID: 2lf0
TitleSolution structure of sf3636, a two-domain unknown function protein from Shigella flexneri 2a, determined by joint refinement of NMR, residual dipolar couplings and small-angle X-ray scattering, NESG target SfR339/OCSP target sf3636
ComponentsUncharacterized protein yibL
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / two-domain protein / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


Uncharacterised protein PF10928, DUF2810 / Protein of unknown function DUF2810 / Protein of unknown function (DUF2810) / UVR domain / DNA Excision Repair, Uvrb; Chain A / Ribosomal Protein S8; Chain: A, domain 1 / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
YibL family ribosome-associated protein / YibL family ribosome-associated protein
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Lemak, A. / Yee, A. / Lee, H. / Gutmanas, A. / Semesi, A. / Garcia, M. / Fang, X. / Wang, Y. / Prestegard, J.H. ...Wu, B. / Lemak, A. / Yee, A. / Lee, H. / Gutmanas, A. / Semesi, A. / Garcia, M. / Fang, X. / Wang, Y. / Prestegard, J.H. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: To be Published
Title: Solution structure of sf3636, a two-domain unknown function protein from Shigella flexneri 2a, determined by joint refinement of NMR, residual dipolar couplings and small-angle X-ray scattering
Authors: Wu, B. / Lemak, A. / Yee, A. / Lee, H. / Gutmanas, A. / Semesi, A. / Garcia, M. / Fang, X. / Wang, Y. / Prestegard, J.H. / Arrowsmith, C.H.
History
DepositionJun 27, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2Nov 7, 2012Group: Database references / Structure summary
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl / pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 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 yibL


Theoretical massNumber of molelcules
Total (without water)14,0771
Polymers14,0771
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein yibL


Mass: 14077.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: yibL, S4132, SF3636 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83J25, UniProt: A0A384KBU4*PLUS

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1923D 1H-13C NOESY
11013D 1H-13C NOESY aromatic
11132D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C; U-100% 15N] sf3636, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 0.01 % NaN3-6, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] sf3636, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 x inhibitor cocktail, 100% D2O100% D2O
30.5 mM [U-7% 13C; U-100% 15N] sf3636, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMsf3636-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
10 uMzinc sulphate-41
10 mMDTT-5[U-100% 2H]1
0.01 %NaN3-61
10 mMbenzamidine-71
1 %inhibitor cocktail-81
0.5 mMsf3636-9[U-100% 13C; U-100% 15N]2
10 mMTRIS-10[U-100% 2H]2
300 mMsodium chloride-112
10 uMzinc sulphate-122
10 mMDTT-13[U-100% 2H]2
0.01 %NaN3-142
10 mMbenzamidine-152
1 %inhibitor cocktail-162
0.5 mMsf3636-17[U-7% 13C; U-100% 15N]3
10 mMTRIS-18[U-100% 2H]3
300 mMsodium chloride-193
10 uMzinc sulphate-203
10 mMDTT-21[U-100% 2H]3
0.01 %NaN3-223
10 mMbenzamidine-233
1 %inhibitor cocktail-243
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas, Arrowsmithprocessing
Sparky3.95Goddarddata analysis
FMCGUI2.4Lemak, Arrowsmithchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
ABACUSLemak, Arrowsmithchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The solution structures were generated using CYANA 3.0 with automated noesy assignments and RDC restraints and further refined by incorporating RDC restraints and SAXS data in restrained ...Details: The solution structures were generated using CYANA 3.0 with automated noesy assignments and RDC restraints and further refined by incorporating RDC restraints and SAXS data in restrained molecular dynamics simulation with the program CNS. Although the current models fit well with both RDCs and SAXS, sf3636 may sample a range of relative domain orientations depending on data types and refinement tools. To further investigate sf3636 domain orientation and its intrinsic dynamic nature, Prestegard lab is developing a new protocol using RCSAs and RDCs from several mediums. Their refined models will be deposited later.
NMR constraintsNOE constraints total: 3059 / NOE intraresidue total count: 600 / NOE long range total count: 765 / NOE medium range total count: 922 / NOE sequential total count: 772 / Hydrogen bond constraints total count: 112 / Protein phi angle constraints total count: 100 / Protein psi angle constraints total count: 100
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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