HEADER RNA 19-DEC-17 6BY4 TITLE SINGLE-STATE 14-MER UUCG TETRALOOP CALCULATED FROM EXACT NOES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(P*GP*GP*CP*AP*CP*UP*UP*CP*GP*GP*UP*GP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA, EXACT NOE, UUCG TETRALOOP, 14-MER HAIRPIN, SINGLE-STATE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.J.NICHOLS,M.A.HENEN,A.BORN,D.STROTZ,P.GUNTERT,B.VOGELI REVDAT 4 15-MAY-24 6BY4 1 REMARK REVDAT 3 14-JUN-23 6BY4 1 REMARK REVDAT 2 17-OCT-18 6BY4 1 JRNL REMARK REVDAT 1 13-JUN-18 6BY4 0 JRNL AUTH P.J.NICHOLS,M.A.HENEN,A.BORN,D.STROTZ,P.GUNTERT,B.VOGELI JRNL TITL HIGH-RESOLUTION SMALL RNA STRUCTURES FROM EXACT NUCLEAR JRNL TITL 2 OVERHAUSER ENHANCEMENT MEASUREMENTS WITHOUT ADDITIONAL JRNL TITL 3 RESTRAINTS. JRNL REF COMMUN BIOL V. 1 61 2018 JRNL REFN ESSN 2399-3642 JRNL PMID 30271943 JRNL DOI 10.1038/S42003-018-0067-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BY4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1000231769. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.4; 6.4 REMARK 210 IONIC STRENGTH : 20; 20 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 20 MM NONE KHPO4, 0.4 MM NONE REMARK 210 EDTA, 1 MM NONE 14-MER UUCG REMARK 210 TETRALOOP, 95% H2O/5% D2O; 20 MM REMARK 210 NONE KHPO4, 0.4 MM NONE EDTA, REMARK 210 1.7 MM NONE 14-MER UUCG REMARK 210 TETRALOOP, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D WATERGATE [1H-1H] NOESY REMARK 210 BUILDUP SERIES; 2D PRESAT [1H-1H] REMARK 210 NOESY BUILDUP SERIES REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN DIRECT DRIVE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, CCPNMR, CYANA 3.98 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: 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 C A 8 O4' C A 8 C4' -0.102 REMARK 500 1 G A 9 O4' G A 9 C4' -0.101 REMARK 500 1 C A 13 O4' C A 13 C4' -0.080 REMARK 500 2 C A 8 O4' C A 8 C4' -0.115 REMARK 500 2 G A 9 O4' G A 9 C4' -0.094 REMARK 500 2 C A 13 O4' C A 13 C4' -0.079 REMARK 500 3 C A 8 O4' C A 8 C4' -0.101 REMARK 500 3 G A 9 O4' G A 9 C4' -0.109 REMARK 500 3 C A 13 O4' C A 13 C4' -0.079 REMARK 500 4 C A 8 O4' C A 8 C4' -0.101 REMARK 500 4 G A 9 O4' G A 9 C4' -0.102 REMARK 500 5 G A 2 O4' G A 2 C4' -0.106 REMARK 500 5 C A 8 O4' C A 8 C4' -0.104 REMARK 500 5 G A 9 O4' G A 9 C4' -0.110 REMARK 500 5 C A 13 O4' C A 13 C4' -0.080 REMARK 500 6 G A 2 O4' G A 2 C4' -0.103 REMARK 500 6 C A 8 O4' C A 8 C4' -0.105 REMARK 500 6 G A 9 O4' G A 9 C4' -0.103 REMARK 500 7 G A 2 O4' G A 2 C4' -0.105 REMARK 500 7 C A 8 O4' C A 8 C4' -0.103 REMARK 500 7 G A 9 O4' G A 9 C4' -0.103 REMARK 500 8 C A 8 O4' C A 8 C4' -0.103 REMARK 500 8 G A 9 O4' G A 9 C4' -0.102 REMARK 500 8 C A 13 O4' C A 13 C4' -0.079 REMARK 500 9 C A 8 O4' C A 8 C4' -0.103 REMARK 500 9 G A 9 O4' G A 9 C4' -0.102 REMARK 500 9 G A 12 O4' G A 12 C4' -0.082 REMARK 500 10 C A 8 O4' C A 8 C4' -0.102 REMARK 500 10 G A 9 O4' G A 9 C4' -0.103 REMARK 500 11 C A 8 O4' C A 8 C4' -0.104 REMARK 500 11 G A 9 O4' G A 9 C4' -0.102 REMARK 500 11 G A 12 O4' G A 12 C4' -0.083 REMARK 500 12 C A 8 O4' C A 8 C4' -0.102 REMARK 500 12 G A 9 O4' G A 9 C4' -0.103 REMARK 500 12 G A 12 O4' G A 12 C4' -0.083 REMARK 500 13 U A 7 O4' U A 7 C4' -0.090 REMARK 500 13 C A 13 O4' C A 13 C4' -0.080 REMARK 500 14 U A 7 O4' U A 7 C4' -0.091 REMARK 500 14 C A 13 O4' C A 13 C4' -0.079 REMARK 500 15 G A 2 O4' G A 2 C4' -0.101 REMARK 500 15 U A 7 O4' U A 7 C4' -0.088 REMARK 500 15 C A 13 O4' C A 13 C4' -0.080 REMARK 500 16 U A 7 O4' U A 7 C4' -0.089 REMARK 500 16 C A 13 O4' C A 13 C4' -0.080 REMARK 500 17 G A 1 O4' G A 1 C4' -0.086 REMARK 500 17 C A 8 O4' C A 8 C4' -0.095 REMARK 500 17 G A 9 O4' G A 9 C4' -0.103 REMARK 500 18 U A 7 O4' U A 7 C4' -0.089 REMARK 500 19 G A 2 O4' G A 2 C4' -0.093 REMARK 500 19 C A 8 O4' C A 8 C4' -0.114 REMARK 500 REMARK 500 THIS ENTRY HAS 56 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 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 G A 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 2 O4' - C4' - C3' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 G A 2 C1' - O4' - C4' ANGL. DEV. = 8.2 DEGREES REMARK 500 1 G A 2 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 2 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 2 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 C A 3 O4' - C4' - C3' ANGL. DEV. = -10.5 DEGREES REMARK 500 1 A A 4 C5' - C4' - O4' ANGL. DEV. = 8.9 DEGREES REMARK 500 1 C A 5 C5' - C4' - O4' ANGL. DEV. = 24.7 DEGREES REMARK 500 1 U A 6 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 U A 7 C1' - O4' - C4' ANGL. DEV. = 5.6 DEGREES REMARK 500 1 C A 8 C1' - O4' - C4' ANGL. DEV. = 7.1 DEGREES REMARK 500 1 G A 9 O4' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 1 G A 9 C1' - O4' - C4' ANGL. DEV. = 6.5 DEGREES REMARK 500 1 G A 9 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 9 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 9 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 10 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 1 G A 10 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 10 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 10 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 U A 11 C5' - C4' - O4' ANGL. DEV. = 12.4 DEGREES REMARK 500 1 U A 11 C1' - O4' - C4' ANGL. DEV. = 6.6 DEGREES REMARK 500 1 G A 12 O4' - C4' - C3' ANGL. DEV. = -9.8 DEGREES REMARK 500 1 G A 12 C1' - O4' - C4' ANGL. DEV. = 6.9 DEGREES REMARK 500 1 G A 12 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 12 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 12 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 C A 13 C1' - O4' - C4' ANGL. DEV. = 8.4 DEGREES REMARK 500 1 C A 14 O4' - C4' - C3' ANGL. DEV. = -10.5 DEGREES REMARK 500 1 C A 14 C1' - O4' - C4' ANGL. DEV. = 5.1 DEGREES REMARK 500 2 G A 1 C1' - O4' - C4' ANGL. DEV. = 8.2 DEGREES REMARK 500 2 G A 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 2 G A 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 G A 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 G A 2 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 2 G A 2 C1' - O4' - C4' ANGL. DEV. = 8.3 DEGREES REMARK 500 2 G A 2 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 2 G A 2 N1 - C2 - N3 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 G A 2 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 C A 3 O4' - C4' - C3' ANGL. DEV. = -10.2 DEGREES REMARK 500 2 C A 3 C5' - C4' - O4' ANGL. DEV. = 5.7 DEGREES REMARK 500 2 A A 4 C5' - C4' - O4' ANGL. DEV. = 9.2 DEGREES REMARK 500 2 A A 4 C1' - O4' - C4' ANGL. DEV. = 5.5 DEGREES REMARK 500 2 C A 5 C5' - C4' - O4' ANGL. DEV. = 25.8 DEGREES REMARK 500 2 U A 6 O4' - C4' - C3' ANGL. DEV. = -6.3 DEGREES REMARK 500 2 U A 6 C1' - O4' - C4' ANGL. DEV. = 7.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 716 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30386 RELATED DB: BMRB REMARK 900 SINGLE-STATE 14-MER UUCG TETRALOOP CALCULATED FROM EXACT NOES DBREF 6BY4 A 1 14 PDB 6BY4 6BY4 1 14 SEQRES 1 A 14 G G C A C U U C G G U G C SEQRES 2 A 14 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