HEADER RNA 14-FEB-09 2KFC OBSLTE 19-JAN-11 2KFC 2L1V TITLE SOLUTION STRUCTURE OF A PREQ1 RIBOSWITCH (CLASS I) APTAMER BOUND TO TITLE 2 PREQ1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (36-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS PREQ1, RIBOSWITCH, RNA, TRANSCRIPTIONAL GENE CONTROL EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.KANG,J.FEIGON REVDAT 4 19-JAN-11 2KFC 1 OBSLTE REVDAT 3 14-APR-09 2KFC 1 JRNL REVDAT 2 07-APR-09 2KFC 1 JRNL REVDAT 1 17-MAR-09 2KFC 0 JRNL AUTH M.KANG,R.PETERSON,J.FEIGON JRNL TITL STRUCTURAL INSIGHTS INTO RIBOSWITCH CONTROL OF THE JRNL TITL 2 BIOSYNTHESIS OF QUEUOSINE, A MODIFIED NUCLEOTIDE FOUND IN JRNL TITL 3 THE ANTICODON OF TRNA. JRNL REF MOL.CELL V. 33 784 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 19285444 JRNL DOI 10.1016/J.MOLCEL.2009.02.019 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH 2.9.8 REMARK 3 AUTHORS : SCHWIETERS, C. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KFC COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-09. REMARK 100 THE RCSB ID CODE IS RCSB101051. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 280 REMARK 210 PH : 6.3; 6.3 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM RNA (36-MER), 2 MM PREQ1, REMARK 210 50 MM POTASSIUM CHLORIDE-3, 90% REMARK 210 H2O/10% D2O; 1 MM RNA (36-MER), 2 REMARK 210 MM PREQ1, 50 MM POTASSIUM REMARK 210 CHLORIDE-6, 100% D2O; 1 MM [U- REMARK 210 13C; U-15N]-ADE RNA (36-MER), 2 REMARK 210 MM PREQ1, 50 MM POTASSIUM REMARK 210 CHLORIDE-9, 100% D2O; 1 MM [U- REMARK 210 13C; U-15N]-CYT RNA (36-MER), 2 REMARK 210 MM PREQ1, 50 MM POTASSIUM REMARK 210 CHLORIDE-12, 100% D2O; 1 MM [U- REMARK 210 13C; U-15N]-GUA RNA (36-MER), 2 REMARK 210 MM PREQ1, 50 MM POTASSIUM REMARK 210 CHLORIDE-15, 100% D2O; 1 MM [U- REMARK 210 13C; U-15N]-URA RNA (36-MER), 2 REMARK 210 MM PREQ1, 50 MM POTASSIUM REMARK 210 CHLORIDE-18, 100% D2O; 1 MM [U- REMARK 210 98% 13C; U-98% 15N] RNA (36-MER), REMARK 210 2 MM PREQ1, 50 MM POTASSIUM REMARK 210 CHLORIDE-21, 90% H2O/10% D2O; 1 REMARK 210 MM [U-13C; U-15N]-URA RNA (36- REMARK 210 MER), 2 MM PREQ1, 50 MM POTASSIUM REMARK 210 CHLORIDE-24, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D DQF-COSY; 2D REMARK 210 1H-1H NOESY; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 2D HNN COSY; 2D HNN REMARK 210 COSY2; 2D 15N CPMG NOESY; 2D REMARK 210 NOESY-11ECHO; 2D H5(C5C4N)H; 2D REMARK 210 FILTERED/EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR_NIH 2.9.8, SPARKY, REMARK 210 XWINNMR, MOLMOL, INSIGHTII REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2' U A 15 H2' A A 16 1.35 REMARK 500 O2' A A 28 H5'' A A 29 1.45 REMARK 500 H22 G A 6 H62 A A 29 1.50 REMARK 500 O2' U A 8 H3' U A 9 1.53 REMARK 500 H22 G A 13 N1 A A 18 1.55 REMARK 500 O2' A A 28 H8 A A 29 1.58 REMARK 500 O2' C A 23 H5' U A 24 1.62 REMARK 500 H1' A A 5 O4 U A 26 1.63 REMARK 500 O2 C A 20 H61 A A 31 1.69 REMARK 500 N3 G A 7 H61 A A 30 1.69 REMARK 500 O2' G A 6 H5' G A 7 1.70 REMARK 500 O2' U A 22 H5' C A 23 1.71 REMARK 500 O6 G A 7 H41 C A 20 1.72 REMARK 500 O6 G A 13 H41 C A 33 1.73 REMARK 500 HO2' C A 20 N1 A A 31 1.73 REMARK 500 O2' A A 16 H5' U A 17 1.73 REMARK 500 N1 A A 12 H3 U A 34 1.73 REMARK 500 H61 A A 5 O4 U A 22 1.75 REMARK 500 O2 C A 21 H61 A A 29 1.78 REMARK 500 HO2' A A 31 O4' A A 32 1.79 REMARK 500 O6 G A 4 H41 C A 23 1.79 REMARK 500 O4' A A 25 H6 U A 26 1.80 REMARK 500 H61 A A 32 N3 PRF A 37 1.80 REMARK 500 O3' G A 2 H8 A A 3 1.80 REMARK 500 H1 G A 4 N3 C A 23 1.81 REMARK 500 H5'' G A 7 OP2 U A 8 1.82 REMARK 500 O2 U A 22 H61 A A 28 1.83 REMARK 500 H21 G A 4 O2 C A 23 1.84 REMARK 500 O4 U A 8 H42 C A 33 1.84 REMARK 500 H22 G A 7 N1 A A 30 1.84 REMARK 500 O2' A A 30 H8 A A 31 1.84 REMARK 500 O2' G A 13 H62 A A 18 1.84 REMARK 500 H2 A A 30 N7 A A 31 1.85 REMARK 500 O2' A A 31 H5'' A A 32 1.86 REMARK 500 O2' A A 27 H8 A A 28 1.86 REMARK 500 O2' C A 20 H5' C A 21 1.89 REMARK 500 H2' G A 6 O4' G A 7 1.89 REMARK 500 N7 G A 7 H112 PRF A 37 1.90 REMARK 500 O2' A A 5 H8 G A 6 1.90 REMARK 500 H2' A A 12 O4' G A 13 1.91 REMARK 500 H4' U A 24 O5' A A 25 1.91 REMARK 500 N1 A A 5 H3 U A 22 1.91 REMARK 500 HO2' U A 34 O4' A A 35 1.91 REMARK 500 O2' A A 3 H5' G A 4 1.94 REMARK 500 N1 A A 3 H3 U A 24 1.94 REMARK 500 H4' G A 1 O5' G A 2 1.95 REMARK 500 HO2' U A 26 OP2 A A 27 1.96 REMARK 500 H2 A A 12 O2 U A 34 1.97 REMARK 500 H22 G A 13 C2 A A 18 1.99 REMARK 500 O2' C A 10 H6 U A 11 2.01 REMARK 500 REMARK 500 THIS ENTRY HAS 1691 CLOSE CONTACTS 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 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 3 C8 - N9 - C4 ANGL. DEV. = -2.4 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. = -2.7 DEGREES REMARK 500 1 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 U A 8 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 U A 8 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 27 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 28 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 29 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 30 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 31 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 32 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 35 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 36 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 3 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 A A 3 C8 - N9 - C4 ANGL. DEV. = -2.4 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. = -2.8 DEGREES REMARK 500 2 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 27 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 28 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 580 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PRF A 37 DBREF 2KFC A 1 36 PDB 2KFC 2KFC 1 36 SEQRES 1 A 36 G G A G A G G U U C U A G SEQRES 2 A 36 U U A U A C C C U C U A U SEQRES 3 A 36 A A A A A A C U A A HET PRF A 37 22 HETNAM PRF 7-DEAZA-7-AMINOMETHYL-GUANINE FORMUL 2 PRF C7 H9 N5 O SITE 1 AC1 5 G A 6 G A 7 U A 8 G A 13 SITE 2 AC1 5 C A 19 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