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- PDB-2jt1: Solution NMR structure of PefI (Plasmid-Encoded Fimbriae Regulato... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jt1 | ||||||
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Title | Solution NMR structure of PefI (Plasmid-Encoded Fimbriae Regulatory) protein from Salmonella typhimurium. Northeast Structural Genomics target StR82 | ||||||
![]() | PefI protein | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Aramini, J.M. / Rossi, P. / Wang, H. / Nwosu, C. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. ...Aramini, J.M. / Rossi, P. / Wang, H. / Nwosu, C. / 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) | ||||||
![]() | ![]() Title: Solution NMR structure of the plasmid-encoded fimbriae regulatory protein PefI from Salmonella enterica serovar Typhimurium. Authors: Aramini, J.M. / Rossi, P. / Cort, J.R. / Ma, L.C. / Xiao, R. / Acton, T.B. / Montelione, G.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 482.7 KB | Display | ![]() |
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PDB format | ![]() | 407 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 8686.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Species: Salmonella typhimurium ![]() Strain: LT2, SGSC1412 / Gene: pefI, PSLT013 / Plasmid: pET21 / Production host: ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING. 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 WERE DETERMINED USING CYANA 2.1. DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.8%, SIDE CHAIN, 95.8%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 71, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 5-19,23-57,66-69: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 95.9%, ADDITIONALLY ALLOWED, 4.1%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.16/0.94, ALL, 0.11/0.65. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 21.29/-2.13. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-71): RECALL, 0.983, PRECISION, 0.930, F-MEASURE, 0.956, DP-SCORE, 0.789. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED (S(PHI) + S(PSI) < 1.8): 1-4,20-22,58-65,70-71. |
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Sample preparation
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Sample conditions | Ionic strength: 450 / pH: 5.5 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: ![]() Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1155 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 92 DIHEDRAL ANGLE CONSTRAINTS, AND 52 HYDROGEN BOND CONSTRAINTS (19.1 ...Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1155 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 92 DIHEDRAL ANGLE CONSTRAINTS, AND 52 HYDROGEN BOND CONSTRAINTS (19.1 CONSTRAINTS PER RESIDUE, 4.5 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 71 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19. | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1273 / NOE intraresidue total count: 358 / NOE long range total count: 345 / NOE medium range total count: 235 / NOE sequential total count: 335 / Protein phi angle constraints total count: 46 / Protein psi angle constraints total count: 46 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.1 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 1.6 ° / Maximum upper distance constraint violation: 0.36 Å / Torsion angle constraint violation method: PDBStat | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.01 Å |