HEADER RNA 01-SEP-05 2AWQ TITLE SOLUTION STRUCTURE OF PSEUDOURIDINE-32 MODIFIED ANTICODON STEM-LOOP OF TITLE 2 E. COLI TRNAPHE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*GP*GP*AP*(PSU) COMPND 3 P*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP*C)-3'; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: ANTICODON ARM; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: PSEUDOURIDINE-MODIFIED ANTICODON ARM OF E. COLI COMPND 8 TRNAPHE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PREPARED BY IN VITRO TRANSCRIPTION AND ENZYMATICALLY SOURCE 4 PSEUDOURIDYLATED KEYWDS TRI-LOOP, WATSON-CRICK TYPE PSI32-A38 BASE PAIR, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.CABELLO-VILLEGAS,E.P.NIKONOWICZ REVDAT 3 09-MAR-22 2AWQ 1 REMARK LINK REVDAT 2 24-FEB-09 2AWQ 1 VERSN REVDAT 1 17-JAN-06 2AWQ 0 JRNL AUTH J.CABELLO-VILLEGAS,E.P.NIKONOWICZ JRNL TITL SOLUTION STRUCTURE OF PSI32-MODIFIED ANTICODON STEM-LOOP OF JRNL TITL 2 ESCHERICHIA COLI TRNAPHE. JRNL REF NUCLEIC ACIDS RES. V. 33 6961 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 16377777 JRNL DOI 10.1093/NAR/GKI1004 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINED USING NOE DERIVED REMARK 3 DISTANCE CONSTRAINTS, AND TORSIONAL ANGLE RESTRAINTS DERIVED REMARK 3 FROM J-COUPLINGS. HYDROGEN BONDS DERIVED FROM NOESY AND NN-COSY REMARK 3 DATA. REMARK 4 REMARK 4 2AWQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034404. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 285 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 10 MM NACL, 10 MM POTASSIUM REMARK 210 PHOSPHATE; 10 MM NACL, 10 MM REMARK 210 POTASSIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2.3 MM C-13 LABELED RNA HAIRPIN, REMARK 210 10 MM NACL, 10 MM POTASSIUM REMARK 210 PHOSPHATE, PH 6.8; 2.8 MM N-15 REMARK 210 LABELED RNA HAIRPIN, 10 MM NACL, REMARK 210 10 MM POTASSIUM PHOSPHATE, PH 6.8 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; HCCH REMARK 210 -TOCSY; CCH-RELAY; 3D_15N- REMARK 210 SEPARATED_NOESY; DQF-COSY; HP- REMARK 210 HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000 REMARK 210 METHOD USED : TORSION ANGLE RANDOMIZATION REMARK 210 SIMULATED ANNEALING AND REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 75 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: PSEUDOURIDINE ASSIGNED USING CCH-RELAY TYPE EXPERIMENTS. REMARK 210 BASE PAIRING DETERMINED FROM INTERRESIDUE N-N SCALAR REMARK 210 CORRELATIONS. DISTANCES DERIVED FROM MULTIPLE MIXING TIME NOESY REMARK 210 EXPERIMENTS. 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 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 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 5 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 9 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 11 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 10 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 11 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 12 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 3 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 3 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 3 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 5 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 3 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 188 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2AWQ A 1 17 PDB 2AWQ 2AWQ 1 17 SEQRES 1 A 17 G G G G A PSU U G A A A A U SEQRES 2 A 17 C C C C MODRES 2AWQ PSU A 6 U PSEUDOURIDINE-5'-MONOPHOSPHATE HET PSU A 6 30 HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE FORMUL 1 PSU C9 H13 N2 O9 P LINK O3' A A 5 P PSU A 6 1555 1555 1.62 LINK O3' PSU A 6 P U A 7 1555 1555 1.62 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