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Yorodumi- PDB-2g7j: Solution NMR structure of the putative cytoplasmic protein ygaC f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g7j | ||||||
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Title | Solution NMR structure of the putative cytoplasmic protein ygaC from Salmonella typhimurium. Northeast Structural Genomics target StR72. | ||||||
Components | putative cytoplasmic protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / StR72 / AUTOSTRUCTURE / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Protein of unknown function DUF2002 / Protein of unknown function DUF2002 / Protein of unknown function (DUF2002) / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / : / Putative cytoplasmic protein Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Aramini, J.M. / Swapna, G.V.T. / Ramelot, T.A. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Shetty, K. / Xiao, R. / Acton, T.B. / Kennedy, M.A. ...Aramini, J.M. / Swapna, G.V.T. / Ramelot, T.A. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Shetty, K. / Xiao, R. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Solution NMR structure of the putative cytoplasmic protein ygaC from Salmonella typhimurium. Northeast Structural Genomics target StR72. Authors: Aramini, J.M. / Swapna, G.V.T. / Ramelot, T.A. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Shetty, K. / Xiao, R. / Acton, T.B. / Kennedy, M.A. / 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 | 2g7j.cif.gz | 695 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g7j.ent.gz | 579 KB | Display | PDB format |
PDBx/mmJSON format | 2g7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g7j_validation.pdf.gz | 348.2 KB | Display | wwPDB validaton report |
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Full document | 2g7j_full_validation.pdf.gz | 491.6 KB | Display | |
Data in XML | 2g7j_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 2g7j_validation.cif.gz | 58.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/2g7j ftp://data.pdbj.org/pub/pdb/validation_reports/g7/2g7j | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 14405.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: ygaC / Plasmid: StR72-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: GenBank: 16421350, UniProt: Q8ZML5*PLUS |
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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. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE 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 HYPER AND TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 100%, SIDE CHAIN, 94.6%, AROMATICS, 91.1%, STEREOSPECIFIC METHYL, 94.4%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 to 112, PSVS 1.2), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 3-43,49-50,55-66,69-71,75-76,88-96,98-109: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 87.4%, ADDITIONALLY ALLOWED, 12.4%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.34/-1.02, ALL, -0.32/-1.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 25.21/-2.80. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.971, PRECISION, 0.945, F-MEASURE, 0.958, DP-SCORE, 0.846. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1759 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 219 DIHEDRAL ANGLE CONSTRAINTS, AND 58 HYDROGEN BOND CONSTRAINTS (18.2 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1759 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 219 DIHEDRAL ANGLE CONSTRAINTS, AND 58 HYDROGEN BOND CONSTRAINTS (18.2 CONSTRAINTS PER RESIDUE, 6.7 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 to 112 BY PSVS 1.2). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE FINAL 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 UNSTRUCTURED C-TERMINUS OF THE PROTEIN (EKTD + LEHHHHHH TAG) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |