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Yorodumi- PDB-2jn8: Solution NMR structure of Q8ZRJ2 from Salmonella typhimurium. Nor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jn8 | ||||||
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Title | Solution NMR structure of Q8ZRJ2 from Salmonella typhimurium. Northeast Structural Genomics target StR65. | ||||||
Components | Putative cytoplasmic protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / PSI-2 / AutoStructure / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | AhpD-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 species | Salmonella typhimurium (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
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. ...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) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jn8.cif.gz | 661.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jn8.ent.gz | 552.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jn8_validation.pdf.gz | 345.8 KB | Display | wwPDB validaton report |
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Full document | 2jn8_full_validation.pdf.gz | 484.2 KB | Display | |
Data in XML | 2jn8_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 2jn8_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/2jn8 ftp://data.pdbj.org/pub/pdb/validation_reports/jn/2jn8 | HTTPS FTP |
-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: 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
-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 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. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 100 / pH: 6.5 / 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
NMR software |
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Refinement | Method: 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 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 |