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Yorodumi- PDB-1yh5: Solution NMR Structure of Protein yggU from Escherichia coli. Nor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yh5 | ||||||
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Title | Solution NMR Structure of Protein yggU from Escherichia coli. Northeast Structural Genomics Consortium Target ER14. | ||||||
Components | ORF, HYPOTHETICAL PROTEIN | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA+BETA / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / PSI / Protein Structure Initiative / NESG | ||||||
Function / homology | Conserved Hypothetical Protein Mth637; Chain: A; / YggU-like / Protein of unknown function DUF167 / YggU-like superfamily / Uncharacterised ACR, YggU family COG1872 / DUF167 / 2-Layer Sandwich / Alpha Beta / UPF0235 protein YggU Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS SIMULATED ANNEALING | ||||||
Authors | Aramini, J.M. / Xiao, R. / Huang, Y.J. / Acton, T.B. / Wu, M.J. / Mills, J.L. / Tejero, R.T. / Szyperski, T. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Solution Structure of the Hypothetical Protein Yggu from E. Coli. Northeast Structural Genomics Consortium Target Er14. Authors: Aramini, J.M. / Xiao, R. / Huang, Y.J. / Acton, T.B. / Wu, M.J. / Mills, J.L. / Tejero, R.T. / Szyperski, T. / Montelione, G.T. #1: Journal: To be Published Title: Protein NMR Recall, Precision, and F-measure scores (RFP Scores): Structure Quality Assessment Measures Based on Information Retrieval Statistics Authors: Huang, Y.J. / Powers, R. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yh5.cif.gz | 333.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yh5.ent.gz | 285.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/1yh5 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/1yh5 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11903.733 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: YGGU / Plasmid: ER14-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21PMGK / References: UniProt: Q8XCU6 |
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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 RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING THE AUTOSTRUCTURE PROGRAM. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED USING HYPER AND TALOS.FINAL STRUCTURE QUALITY FACTORS FOR THE ENSEMBLE, WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 8-23,28-29,31-34,37-41,44-65,67-77,80-87: (A) RMSD FOR ORDERED RESIDUES: BB, 0.7 ANG; HEAVY ATOM, 1.2 ANG. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED: 75.9%; ADDITIONALLY ALLOWED: 23.0%; GENEROUSLY ALLOWED, 1.0%; DISALLOWED, 0.2% (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): BB, -1.14/-2.23; ALL, -1.0/-4.17. (D) MAGE MOLPROBITY CLASH SCORE (RAW/Z): 33.22/-4.18 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: F-MEASURE, 0.944; RECALL, 0.977; PRECISION, 0.802; DP-SCORE, 0.726. |
-Sample preparation
Details | Contents: 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5 |
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Sample conditions | Ionic strength: 50 mM NACL / pH: 6.5 / Pressure: AMBIENT / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS SIMULATED ANNEALING / Software ordinal: 1 Details: THE STRUCTURE IS BASED ON A TOTAL OF 1031 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 207 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (12.6 CONSTRAINTS ...Details: THE STRUCTURE IS BASED ON A TOTAL OF 1031 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 207 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (12.6 CONSTRAINTS PER RESIDUE; 4.1 LONG-RANGE CONTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE WITH XPLOR. | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 56 / Conformers submitted total number: 10 |