- PDB-1qkh: SOLUTION STRUCTURE OF THE RIBOSOMAL PROTEIN S19 FROM THERMUS THER... -
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Entry
Database: PDB / ID: 1qkh
Title
SOLUTION STRUCTURE OF THE RIBOSOMAL PROTEIN S19 FROM THERMUS THERMOPHILUS
Components
30S RIBOSOMAL PROTEIN S19
Keywords
RIBOSOMAL PROTEIN / RIBOSOME / THERMUS THERMOPHILUS / S19
Function / homology
Function and homology information
ribosomal small subunit assembly / cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation Similarity search - Function
30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S19, bacterial-type / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURE WAS DETERMINED USING 1104 DISTANCE RESTRAINTS, 42 DIHEDRAL ANGLE RESTRAINTS AND 14 HYDROGEN BOND RESTRAINTS. 50 STRUCTURES WERE CALCULATED AND REFINED USING AN AB INITIO ...Details: THE STRUCTURE WAS DETERMINED USING 1104 DISTANCE RESTRAINTS, 42 DIHEDRAL ANGLE RESTRAINTS AND 14 HYDROGEN BOND RESTRAINTS. 50 STRUCTURES WERE CALCULATED AND REFINED USING AN AB INITIO SIMULATED ANNEALING PROTOCOL FOR X- PLOR AND THEN REFINED IN TWO STEPS. AN R-6 AVERAGING PROTOCOL WAS USED FOR NON-STEREOSPECIFICALLY ASSIGNED PROTONS [1]. DURING THE SIMULATED ANNEALING STEP AND THE FIRST REFINEMENT STEP ONLY THE REPULSIVE PART OF THE VAN DER WAALS INTERACTION WAS INCLUDED. IN THE SECOND REFINEMENT STEP THE VAN DER WAALS INTERACTION WAS PARAMETERIZED USING A LENNARD-JONES POTENTIAL INCLUDING THE ATTRACTIVE PART. 21 STRUCTURES WERE SELECTED ON THE BASIS OF CUMULATIVE RMSD VALUES OF STRUCTURES, ORDERED AFTER OVERALL ENERGY, AND RAMACHANDRAN BEHAVIOR FOR REGIONS WITH LOW RESTRAINT DENSITIES. [1] BRUNGER, A. T., CLORE, G. M., GRONENBORN, A. M. & KARPLUS, M. (1986). THREE-DIMENSIONAL STRUCTURE OF PROTEINS DETERMINED BY MOLECULAR DYNAMICS WITH INTERPROTON DISTANCE RESTRAINTS: APPLICATION TO CRAMBIN. PROC NATL ACAD SCI USA 83, 3801-3805. OTHER DETAILS OF STRUCTURE REFINEMENT CAN BE FOUND IN THE JRNL CITATION.
NMR ensemble
Conformer selection criteria: CUMULATIVE RMSD OF STRUCTURES SORTED AFTER TOTAL ENERGY Conformers calculated total number: 50 / Conformers submitted total number: 21
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