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- PDB-2jn8: Solution NMR structure of Q8ZRJ2 from Salmonella typhimurium. Nor... -

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Basic information

Entry
Database: PDB / ID: 2jn8
TitleSolution NMR structure of Q8ZRJ2 from Salmonella typhimurium. Northeast Structural Genomics target StR65.
ComponentsPutative cytoplasmic proteinCytoplasm
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / PSI-2 / AutoStructure / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyAhpD-like - #30 / Protein of unknown function DUF1889 / YoaC-like superfamily / Domain of unknown function (DUF1889) / AhpD-like / Up-down Bundle / Mainly Alpha / Cytoplasmic protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Cort, J.R. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. ...Aramini, J.M. / Cort, J.R. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of Q8ZRJ2 from Salmonella typhimurium. Northeast Structural Genomics target StR65.
Authors: Aramini, J.M. / Cort, J.R. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionDec 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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_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 / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytoplasmic protein


Theoretical massNumber of molelcules
Total (without water)12,9441
Polymers12,9441
Non-polymers00
Water0
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 Putative cytoplasmic protein / Cytoplasm


Mass: 12943.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: STM0327 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q8ZRJ2

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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-15N NOESY
1413D 1H-13C NOESY
1513D (H)CCH-COSY
1613D (H)CCH-TOCSY
1713D TR backbone expts
1813D TR backbone expts
192high resolution 2D 1H-13C HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 96.9%, SIDE CHAIN, 95.7%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 83.3%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 2 TO 110, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 12-20,32-64,68-84,96-109: (A) RMSD (ORDERED RESIDUES): BB, 0.8, HEAVY ATOM, 1.2. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 96.1%, ADDITIONALLY ALLOWED, 3.9%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.36/1.73, ALL, 0.19/1.12. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 19.96/-1.90. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.976, PRECISION, 0.913, F-MEASURE, 0.944, DP-SCORE, 0.762.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.17 mM [U-100% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
20.89 mM [U-5% 13C, U-100% 15N] StR65, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.17 mMStR65[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMNaCl1
5 mMCaCl21
10 mMDTT1
0.02 %sodium azide1
0.89 mMStR65[U-5% 13C; U-100% 15N]2
20 mMMES2
100 mMNaCl2
5 mMCaCl22
10 mMDTT2
0.02 %sodium azide2
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / 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
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Bruker AMXBrukerAMX6003
Varian INOVAVarianINOVA5004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
BrukerXWINNMR 3.5pl6Brukercollection
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski, Montelionedata analysis
Sparky3.11Goddardprocessing
Sparky3.11Goddarddata analysis
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
AutoStructure2.1.1Huang, Tejero, Powers and Montelionerefinement
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PdbStat4.1Tejero and Montelionedata analysis
PSVS1.3Bhattacharya, Hang and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1218 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 128 DIHEDRAL ANGLE CONSTRAINTS, AND 84 HYDROGEN BOND CONSTRAINTS (13.1 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1218 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 128 DIHEDRAL ANGLE CONSTRAINTS, AND 84 HYDROGEN BOND CONSTRAINTS (13.1 CONSTRAINTS PER RESIDUE, 2.4 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 2 TO 110 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE N-TERMINAL MET AND UNSTRUCTURED C-TERMINUS OF THE PROTEIN (HHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. Coordinates for the following residues are not well determined (S(PHI) + S(PSI) < 1.8): 1-11,21-31,65-67,85-95,110-115.
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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