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- PDB-1xhs: Solution NMR Structure of Protein ytfP from Escherichia coli. Nor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xhs | ||||||
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Title | Solution NMR Structure of Protein ytfP from Escherichia coli. Northeast Structural Genomics Consortium Target ER111. | ||||||
![]() | Hypothetical UPF0131 protein ytfP | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ER111 / AUTOSTRUCTURE / Northeast Structural Genomics Consortium / NESG / Protein Structure Initiative / PSI | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Aramini, J.M. / Huang, Y.J. / Swapna, G.V.T. / Paranji, R.K. / Xiao, R. / Shastry, R. / Acton, T.B. / Cort, J.R. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family. Authors: Aramini, J.M. / Huang, Y.J. / Swapna, G.V. / Cort, J.R. / Rajan, P.K. / Xiao, R. / Shastry, R. / Acton, T.B. / Liu, J. / Rost, B. / Kennedy, M.A. / Montelione, G.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 356 KB | Display | ![]() |
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PDB format | ![]() | 293.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 345.9 KB | Display | ![]() |
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Full document | ![]() | 419.4 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 13952.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ASSIGNMENTS AS ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING HYPER AND TALOS.Completeness of NMR assignments: backbone, 97%; side chain, 91%; stereospecific methyl, 100%. Final structure quality factors for the ensemble, where ordered residues [S(PHI) + S(PSI) > 1.8] comprise 1-5,9-10,17-18,23-38,41-70,76-85,88-93,101-104,106-108: (a) RMSD for ordered residues: BB, 0.7; heavy atom, 1.2. (b) Ramachandran statistics for ordered residues: most favored: 89.9%; additionally allowed: 10.1%; generously allowed, 0.0%; disallowed, 0.0% (c) Procheck scores for ordered residues (raw/Z-): BB, -0.53/-1.77; all, -0.49/-2.90. (d) MAGE Molprobity clash score (raw/Z-): 28.47/-3.36. (e) RPF scores for goodness of fit to NOESY data: F-measure, 0.916; Recall, 0.962; Precision, 0.874; DP-score, 0.791. |
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Sample preparation
Details | Contents: 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C ...Contents: 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O |
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Sample conditions | Ionic strength: 100 mM NACL / pH: 5.5 / Pressure: AMBIENT / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||
NMR spectrometer |
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Processing
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NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1717 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 211 DIHEDRAL ANGLE CONSTRAINTS, AND 68 HYDROGEN BOND CONSTRAINTS (17.2 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1717 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 211 DIHEDRAL ANGLE CONSTRAINTS, AND 68 HYDROGEN BOND CONSTRAINTS (17.2 CONSTRAINTS PER RESIDUE; 6.9 LONG-RANGE CONSTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR). THE 10 LOWEST ENERGY STRUCTURES WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 56 / Conformers submitted total number: 10 |