HEADER RNA 14-APR-09 2KHY TITLE SPECIFIER DOMAIN OF B. SUBTILIS TYRS T BOX LEADER RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (38-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS SPECIFIER DOMAIN, BACILLUS, S-TURN, LOOP-E, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.WANG,T.M.HENKIN REVDAT 3 16-MAR-22 2KHY 1 REMARK REVDAT 2 16-JUN-10 2KHY 1 JRNL REVDAT 1 16-FEB-10 2KHY 0 JRNL AUTH J.WANG,T.M.HENKIN,E.P.NIKONOWICZ JRNL TITL NMR STRUCTURE AND DYNAMICS OF THE SPECIFIER LOOP DOMAIN FROM JRNL TITL 2 THE BACILLUS SUBTILIS TYRS T BOX LEADER RNA. JRNL REF NUCLEIC ACIDS RES. V. 38 3388 2010 JRNL REFN ISSN 0305-1048 JRNL PMID 20110252 JRNL DOI 10.1093/NAR/GKQ020 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.J.GRUNDY,S.E.HODIL,S.M.ROLLINS,T.M.HENKIN REMARK 1 TITL SPECIFICITY OF TRNA-MRNA INTERACTIONS IN BACILLUS SUBTILIS REMARK 1 TITL 2 TYRS ANTITERMINATION. REMARK 1 REF J.BACTERIOL. V. 179 2587 1997 REMARK 1 REFN ISSN 0021-9193 REMARK 1 PMID 9098057 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, C. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KHY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000101143. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301; 287 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 0.020; 0.020 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.8 MM SPECIFIER DOMAIN OF TYRS REMARK 210 T BOX LEADER RNA-1, 100% D2O; REMARK 210 1.6 MM [U-99% 13C; U-99% 15N] REMARK 210 SPECIFIER DOMAIN OF TYRS T BOX REMARK 210 LEADER RNA-2, 93% H2O/7% D2O; REMARK 210 1.6 MM [U-99% 13C; U-99% 15N] REMARK 210 SPECIFIER DOMAIN OF TYRS T BOX REMARK 210 LEADER RNA-3, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 3D 1H-13C NOESY; REMARK 210 3D HCCH-COSY; 3D HCCH-TOCSY; 2D REMARK 210 1H-1H NOESY; 2D DQF-COSY; 2D 1H- REMARK 210 15N HSQC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: FOR ANISOTROPIC EXPERIMENTS, PHAGE PF1 AT 21 MG/ML WAS REMARK 210 USED. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 G A 1 C5' G A 1 C4' 0.117 REMARK 500 1 G A 1 C4' G A 1 C3' 0.069 REMARK 500 1 G A 1 C3' G A 1 C2' 0.083 REMARK 500 1 G A 1 O4' G A 1 C1' 0.077 REMARK 500 1 G A 1 C1' G A 1 N9 0.121 REMARK 500 1 G A 1 C8 G A 1 N9 0.060 REMARK 500 1 G A 2 P G A 2 O5' 0.067 REMARK 500 1 G A 2 C5' G A 2 C4' 0.134 REMARK 500 1 G A 2 C3' G A 2 C2' 0.080 REMARK 500 1 G A 2 O4' G A 2 C1' 0.104 REMARK 500 1 G A 2 C1' G A 2 N9 0.095 REMARK 500 1 G A 2 N1 G A 2 C2 0.054 REMARK 500 1 G A 2 N9 G A 2 C4 0.074 REMARK 500 1 G A 3 P G A 3 O5' 0.077 REMARK 500 1 G A 3 C5' G A 3 C4' 0.139 REMARK 500 1 G A 3 C3' G A 3 C2' 0.089 REMARK 500 1 G A 3 O4' G A 3 C1' 0.101 REMARK 500 1 G A 3 C1' G A 3 N9 0.119 REMARK 500 1 A A 4 P A A 4 O5' 0.078 REMARK 500 1 A A 4 C5' A A 4 C4' 0.132 REMARK 500 1 A A 4 C3' A A 4 C2' 0.090 REMARK 500 1 A A 4 O4' A A 4 C1' 0.116 REMARK 500 1 A A 4 C1' A A 4 N9 0.134 REMARK 500 1 A A 4 C2' A A 4 O2' 0.067 REMARK 500 1 A A 4 N7 A A 4 C8 -0.045 REMARK 500 1 A A 4 N9 A A 4 C4 0.056 REMARK 500 1 U A 5 P U A 5 O5' 0.070 REMARK 500 1 U A 5 C5' U A 5 C4' 0.137 REMARK 500 1 U A 5 C3' U A 5 C2' 0.080 REMARK 500 1 U A 5 O4' U A 5 C1' 0.121 REMARK 500 1 U A 5 C1' U A 5 N1 0.143 REMARK 500 1 U A 5 C4 U A 5 O4 -0.070 REMARK 500 1 U A 5 N1 U A 5 C2 0.089 REMARK 500 1 U A 5 N1 U A 5 C6 0.072 REMARK 500 1 C A 6 C5' C A 6 C4' 0.127 REMARK 500 1 C A 6 C3' C A 6 C2' 0.086 REMARK 500 1 C A 6 O4' C A 6 C1' 0.115 REMARK 500 1 C A 6 C1' C A 6 N1 0.180 REMARK 500 1 C A 6 N1 C A 6 C6 0.038 REMARK 500 1 C A 6 N3 C A 6 C4 -0.042 REMARK 500 1 A A 7 C5' A A 7 C4' 0.116 REMARK 500 1 A A 7 C3' A A 7 C2' 0.074 REMARK 500 1 A A 7 O4' A A 7 C1' 0.090 REMARK 500 1 A A 7 C1' A A 7 N9 0.110 REMARK 500 1 A A 7 N9 A A 7 C4 0.063 REMARK 500 1 C A 8 P C A 8 O5' 0.062 REMARK 500 1 C A 8 C5' C A 8 C4' 0.149 REMARK 500 1 C A 8 C3' C A 8 C2' 0.088 REMARK 500 1 C A 8 O4' C A 8 C1' 0.150 REMARK 500 1 C A 8 C1' C A 8 N1 0.205 REMARK 500 REMARK 500 THIS ENTRY HAS 2615 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 G A 2 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 G A 2 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 G A 3 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 1 A A 4 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 A A 4 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 1 U A 5 C6 - N1 - C2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 U A 5 C5 - C4 - O4 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 U A 5 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 1 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 C A 6 C6 - N1 - C2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 6 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 1 A A 7 P - O5' - C5' ANGL. DEV. = 10.5 DEGREES REMARK 500 1 A A 7 C1' - O4' - C4' ANGL. DEV. = 5.2 DEGREES REMARK 500 1 A A 7 C3' - C2' - C1' ANGL. DEV. = 5.6 DEGREES REMARK 500 1 A A 7 O4' - C1' - N9 ANGL. DEV. = 8.9 DEGREES REMARK 500 1 A A 7 C8 - N9 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 A A 7 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 1 C A 8 C6 - N1 - C2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 8 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 C A 8 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 1 A A 9 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 1 A A 9 O4' - C1' - N9 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 A A 9 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 A A 9 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 A A 10 P - O5' - C5' ANGL. DEV. = 13.0 DEGREES REMARK 500 1 A A 10 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 A A 10 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 A A 10 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 1 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 G A 11 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 1 U A 12 C6 - N1 - C2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 U A 12 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 U A 12 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES REMARK 500 1 A A 13 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 A A 13 C5 - N7 - C8 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 13 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 A A 13 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 G A 14 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 G A 15 N9 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 G A 15 N3 - C4 - N9 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 A A 16 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 C A 17 C6 - N1 - C2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 17 C2 - N3 - C4 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C A 17 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 U A 18 P - O5' - C5' ANGL. DEV. = 10.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1129 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 C A 6 0.07 SIDE CHAIN REMARK 500 1 U A 12 0.10 SIDE CHAIN REMARK 500 1 U A 18 0.12 SIDE CHAIN REMARK 500 1 U A 19 0.11 SIDE CHAIN REMARK 500 1 G A 22 0.08 SIDE CHAIN REMARK 500 1 G A 26 0.14 SIDE CHAIN REMARK 500 1 U A 35 0.07 SIDE CHAIN REMARK 500 1 U A 37 0.08 SIDE CHAIN REMARK 500 2 C A 6 0.07 SIDE CHAIN REMARK 500 2 A A 10 0.06 SIDE CHAIN REMARK 500 2 U A 12 0.10 SIDE CHAIN REMARK 500 2 G A 15 0.07 SIDE CHAIN REMARK 500 2 U A 18 0.11 SIDE CHAIN REMARK 500 2 U A 19 0.11 SIDE CHAIN REMARK 500 2 G A 22 0.08 SIDE CHAIN REMARK 500 2 G A 26 0.09 SIDE CHAIN REMARK 500 2 U A 37 0.09 SIDE CHAIN REMARK 500 3 C A 6 0.08 SIDE CHAIN REMARK 500 3 A A 7 0.05 SIDE CHAIN REMARK 500 3 G A 11 0.09 SIDE CHAIN REMARK 500 3 U A 12 0.07 SIDE CHAIN REMARK 500 3 G A 15 0.07 SIDE CHAIN REMARK 500 3 U A 18 0.15 SIDE CHAIN REMARK 500 3 C A 20 0.09 SIDE CHAIN REMARK 500 3 G A 21 0.06 SIDE CHAIN REMARK 500 3 C A 25 0.07 SIDE CHAIN REMARK 500 3 G A 26 0.10 SIDE CHAIN REMARK 500 3 U A 37 0.08 SIDE CHAIN REMARK 500 4 C A 6 0.08 SIDE CHAIN REMARK 500 4 A A 7 0.06 SIDE CHAIN REMARK 500 4 U A 12 0.13 SIDE CHAIN REMARK 500 4 A A 13 0.07 SIDE CHAIN REMARK 500 4 G A 15 0.06 SIDE CHAIN REMARK 500 4 U A 18 0.12 SIDE CHAIN REMARK 500 4 U A 19 0.11 SIDE CHAIN REMARK 500 4 G A 22 0.08 SIDE CHAIN REMARK 500 4 G A 26 0.11 SIDE CHAIN REMARK 500 4 U A 37 0.07 SIDE CHAIN REMARK 500 5 C A 6 0.07 SIDE CHAIN REMARK 500 5 A A 10 0.06 SIDE CHAIN REMARK 500 5 G A 11 0.07 SIDE CHAIN REMARK 500 5 U A 12 0.08 SIDE CHAIN REMARK 500 5 U A 18 0.12 SIDE CHAIN REMARK 500 5 U A 19 0.10 SIDE CHAIN REMARK 500 5 G A 26 0.08 SIDE CHAIN REMARK 500 5 U A 37 0.10 SIDE CHAIN REMARK 500 6 U A 12 0.08 SIDE CHAIN REMARK 500 6 U A 18 0.13 SIDE CHAIN REMARK 500 6 U A 19 0.10 SIDE CHAIN REMARK 500 6 G A 22 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 95 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2KHY A 1 38 PDB 2KHY 2KHY 1 38 SEQRES 1 A 38 G G G A U C A C A A G U A SEQRES 2 A 38 G G A C U U C G G U C C G SEQRES 3 A 38 A A U A C A G A U C U C CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1