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- PDB-2oa4: Solution NMR Structure: Northeast Structural Genomics Consortium ... -

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Basic information

Entry
Database: PDB / ID: 2oa4
TitleSolution NMR Structure: Northeast Structural Genomics Consortium Target SiR5
ComponentsSiR5
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SiR5 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


sequence-specific DNA binding
Similarity search - Function
Protein of unknown function DUF1153 / Protein of unknown function (DUF1153) / Trp repressor/replication initiator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DUF1153 domain-containing protein
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodSOLUTION NMR
AuthorsWang, L. / Rossi, P. / Chen, C.X. / Nwosu, C. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. ...Wang, L. / Rossi, P. / Chen, C.X. / Nwosu, C. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Burkhard, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target SiR5
Authors: Wang, L. / Rossi, P. / Chen, C.X. / Nwosu, C. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Burkhard, R. / Montelione, G.T.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Authors state that the residue 59 is a Thr. This discrepancy could possibly be due to a ...SEQUENCE Authors state that the residue 59 is a Thr. This discrepancy could possibly be due to a naturally occuring polymorphism, an error in the sequence database, or a mutation in their specific clone

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SiR5


Theoretical massNumber of molelcules
Total (without water)11,4771
Polymers11,4771
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 SiR5


Mass: 11477.274 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Gene: SPO1678 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 / References: UniProt: Q5LST8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131(H)CCH-TOCSY
141(H)CCH-COSY
151CC(CO)NH-TOCSY
1613D HN(CA)CB
171HN(CO)CACB
181HBHA(CO)NH
191HNCA
1101HNCO
1112C13 HSQC noct Stereospecific VL Me assign
1122Het-NOE, T1/Tirho
1131C13 Aromatic NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM U-13C, 15N SiR5, 5% D2O, 95% H2O5% D2O, 95% H2O
21.150mM 5%-13C, 15N SiR5, 5% D2O, 95% H2O5% D2O, 95% H2O
Sample conditionsIonic strength: 0.1M NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
XwinNMR3.5Bruker Biospincollection
DYANA1.2structure solution
X-PLOR2.11.2refinement
NMRPipe2005Delaglioprocessing
AutoAssign2.2.1Moseley et al.structure solution
AutoStructure2.1.1Huang et al.structure solution
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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