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- PDB-2jrp: Solution NMR Structure of YfgJ from Salmonella typhimurium Modele... -

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Basic information

Entry
Database: PDB / ID: 2jrp
TitleSolution NMR Structure of YfgJ from Salmonella typhimurium Modeled with Two Zn+2 Bound, Northeast Structural Genomics Consortium Target StR86
ComponentsPutative cytoplasmic protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / two-zinc binding protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyRubredoxin-like / YfgJ-like / DUF1407/YfgJ-like / DUF1407/YfgJ-like superfamily / zinc-ribbons / Ribbon / Mainly Beta / Putative cytoplasmic protein
Function and homology information
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsDing, K. / Ramelot, T.A. / Cort, J.R. / Wang, H. / Nwosu, C. / Cunningham, K. / Owens, L. / Ma, L. / Xiao, R. / Liu, J. ...Ding, K. / Ramelot, T.A. / Cort, J.R. / Wang, H. / Nwosu, C. / Cunningham, K. / Owens, L. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of YfgJ from Salmonella typhimurium Modeled with Two Zn+2 Bound.
Authors: Ding, K. / Ramelot, T.A. / Cort, J.R. / Wang, H. / Nwosu, C. / Cunningham, K. / Owens, L. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 28, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2923
Polymers9,1611
Non-polymers1312
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 / 25structures with the lowest bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative cytoplasmic protein


Mass: 9161.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Species: Salmonella typhimurium / Strain: LT2, SGSC1412 / Gene: yfgJ, STM2518 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZN54
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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
1332D 1H-13C HSQC
1413D HNCO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HNHA
1913D (H)CCH-TOCSY
11013D C(CO)NH
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11323D 1H-13C NOESY
11423D aromatic 1H-13C NOESY
11524D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] protein, 20 mM NH4OAc, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] protein, 20 mM NH4OAc, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % NaN3, 100% D2O100% D2O
31.7 mM [U-5% 13C; U-100% 15N] protein, 20 mM NH4OAc, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-100% 13C; U-100% 15N]1
20 mMNH4OAc1
100 mMNaCl1
10 mMDTT1
5 mMCaCl21
0.02 %NaN31
1 mMprotein[U-100% 13C; U-100% 15N]2
20 mMNH4OAc2
100 mMNaCl2
10 mMDTT2
5 mMCaCl22
0.02 %NaN32
1.7 mMprotein[U-5% 13C; U-100% 15N]3
20 mMNH4OAc3
100 mMNaCl3
10 mMDTT3
5 mMCaCl23
0.02 %NaN33
Sample conditionsIonic strength: 100 / pH: 4.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
AutoStructure2.1.1Huang, Tejero, Powers and Montelionedata analysis
Sparky3.1Goddardpeak picking
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: DGSA using xplor NIH and then followed by cns water refinement.
NMR constraintsNOE constraints total: 430 / NOE long range total count: 238 / NOE medium range total count: 68 / NOE sequential total count: 124 / Protein phi angle constraints total count: 27 / Protein psi angle constraints total count: 27
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest bond energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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