HEADER RNA 05-DEC-13 2MI0 TITLE NMR STRUCTURE OF THE I-V KISSING-LOOP INTERACTION OF THE NEUROSPORA VS TITLE 2 RIBOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP COMPND 3 *CP*UP*CP*A)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP COMPND 8 *CP*GP*C)-3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: NEUROSPORA; SOURCE 4 ORGANISM_TAXID: 5140; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: NEUROSPORA; SOURCE 8 ORGANISM_TAXID: 5140 KEYWDS NEUROSPORA VS RIBOZYME, KISSING-LOOP INTERACTION, SUBSTRATE KEYWDS 2 RECOGNITION, U-TURN, NMR STRUCTURAL STUDIES, RNA EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR P.BOUCHARD,P.LEGAULT REVDAT 3 01-MAY-24 2MI0 1 REMARK REVDAT 2 29-JAN-14 2MI0 1 JRNL REVDAT 1 15-JAN-14 2MI0 0 JRNL AUTH P.BOUCHARD,P.LEGAULT JRNL TITL STRUCTURAL INSIGHTS INTO SUBSTRATE RECOGNITION BY THE JRNL TITL 2 NEUROSPORA VARKUD SATELLITE RIBOZYME: IMPORTANCE OF U-TURNS JRNL TITL 3 AT THE KISSING-LOOP JUNCTION. JRNL REF BIOCHEMISTRY V. 53 258 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24325625 JRNL DOI 10.1021/BI401491G REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MI0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103637. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 288 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 50 MM NACL, 5 MM MGCL2; 50 MM REMARK 210 NACL, 5 MM MGCL2 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.3-2.2 MM 5' REMARK 210 -R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP* REMARK 210 CP*A)-3', 1.3-2.2 MM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP* REMARK 210 AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 MM [U-2H] TRIS, 50 MM REMARK 210 SODIUM CHLORIDE, 0.05 MM SODIUM AZIDE, 5 MM MAGNESIUM CHLORIDE, REMARK 210 90% H2O/10% D2O; 1.5 MM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP* REMARK 210 UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.5 MM [U-13C; U-15N] 5'-R(* REMARK 210 GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3' REMARK 210 , 10 MM [U-2H] TRIS, 50 MM SODIUM CHLORIDE, 0.05 MM SODIUM AZIDE, REMARK 210 5 MM MAGNESIUM CHLORIDE, 100% D2O; 1.4 MM [U-15N] 5'-R(*GP*AP* REMARK 210 GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', REMARK 210 1.4 MM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP* REMARK 210 UP*CP*GP*C)-3', 10 MM [U-2H] TRIS, 50 MM SODIUM CHLORIDE, 0.05 REMARK 210 MM SODIUM AZIDE, 5 MM MAGNESIUM CHLORIDE, 90% H2O/10% D2O; 1.7 REMARK 210 MM [U-13C; U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP* REMARK 210 GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.7 MM 5'-R(*GP*CP*GP*GP*CP*AP*GP* REMARK 210 UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 MM [U-2H] TRIS, REMARK 210 50 MM SODIUM CHLORIDE, 0.05 MM SODIUM AZIDE, 5 MM MAGNESIUM REMARK 210 CHLORIDE, 100% D2O; 1.4 MM [U-13C; U-15N]-GUA 5'-R(*GP*AP*GP*CP* REMARK 210 AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 MM REMARK 210 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP* REMARK 210 GP*C)-3', 10 MM [U-2H] TRIS, 50 MM SODIUM CHLORIDE, 0.05 MM REMARK 210 SODIUM AZIDE, 5 MM MAGNESIUM CHLORIDE, 100% D2O; 1.4 MM [U-13C; REMARK 210 U-15N]-GUA 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP* REMARK 210 UP*GP*CP*UP*CP*A)-3', 1.4 MM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP* REMARK 210 AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 MM [U-2H] TRIS, 50 MM REMARK 210 SODIUM CHLORIDE, 0.05 MM SODIUM AZIDE, 5 MM MAGNESIUM CHLORIDE, REMARK 210 100% D2O; 1.4 MM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP* REMARK 210 UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 MM 5'-R(*GP*CP*GP*GP*CP* REMARK 210 AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 MM [U-2H] REMARK 210 TRIS, 50 MM SODIUM CHLORIDE, 0.05 MM SODIUM AZIDE, 5 MM REMARK 210 MAGNESIUM CHLORIDE, 100% D2O; 1.3 MM 5'-R(*GP*AP*GP*CP*AP*GP*CP* REMARK 210 AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3 MM [U-15N] REMARK 210 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP* REMARK 210 GP*C)-3', 10 MM [U-2H] TRIS, 50 MM SODIUM CHLORIDE, 0.05 MM REMARK 210 SODIUM AZIDE, 5 MM MAGNESIUM CHLORIDE, 100% D2O; 1.7 MM [U-13C; REMARK 210 U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP* REMARK 210 GP*CP*UP*CP*A)-3', 1.7 MM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP* REMARK 210 CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 MM [U-2H] TRIS, 50 MM REMARK 210 SODIUM CHLORIDE, 0.05 MM SODIUM AZIDE, 5 MM MAGNESIUM CHLORIDE, REMARK 210 90% H2O/10% D2O; 1.5 MM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP* REMARK 210 UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.5 MM [U-13C; U-15N] 5'-R(* REMARK 210 GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3' REMARK 210 , 10 MM [U-2H] TRIS, 50 MM SODIUM CHLORIDE, 0.05 MM SODIUM AZIDE, REMARK 210 5 MM MAGNESIUM CHLORIDE, 90% H2O/10% D2O; 0.2-0.3 MM [U-15N] 5'- REMARK 210 R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP* REMARK 210 CP*A)-3', 0.2-0.3 MM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP* REMARK 210 AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 MM [U-2H] TRIS, 50 MM REMARK 210 SODIUM CHLORIDE, 0.05 MM SODIUM AZIDE, 5 MM MAGNESIUM CHLORIDE, REMARK 210 14.6-20.5 MG/ML PF1 PHAGE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N HSQC REMARK 210 NH2 ONLY; 2D 1H-15N NHH COSY; 2D REMARK 210 1H-15N HMQC J=21HZ; 2D 1H-15N REMARK 210 CPMG NOESY; 2D 1H-1H FLIP-BACK REMARK 210 WATERGATE NOESY; 3D 15N-EDITED REMARK 210 NOESY-HSQC; 2D 1H-13C CT-HSQC; REMARK 210 3D 15N/13C-EDITED NOESY-HSQC; 3D REMARK 210 13C-EDITED HMQC-NOESY; 3D HCCH- REMARK 210 COSY; 1D 15N-DECOUPLED 1H REMARK 210 WATERGATE; 1D 15N-FILTERED 1H REMARK 210 WATERGATE; 1D 15N-EDITED 1H REMARK 210 WATERGATE REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, X-PLOR NIH, PYMOL, REMARK 210 CCPNMR_SUITE, CURVES+ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 2 N7 - C8 - N9 ANGL. DEV. = 3.7 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. = -2.6 DEGREES REMARK 500 1 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 18 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G B 101 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 101 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G B 103 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G B 103 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G B 104 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 104 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A B 106 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G B 107 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G B 107 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G B 110 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 110 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A B 111 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A B 114 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G B 117 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 117 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G B 120 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G B 120 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 2 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 735 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19662 RELATED DB: BMRB DBREF 2MI0 A 1 22 PDB 2MI0 2MI0 1 22 DBREF 2MI0 B 101 121 PDB 2MI0 2MI0 101 121 SEQRES 1 A 22 G A G C A G C A U C G U C SEQRES 2 A 22 G G C U G C U C A SEQRES 1 B 21 G C G G C A G U U G A C U SEQRES 2 B 21 A C U G U C G 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