HEADER RNA 07-APR-98 1A9L TITLE SOLUTION STRUCTURE OF A SUBSTRATE FOR THE ARCHAEAL PRE-TRNA SPLICING TITLE 2 ENDONUCLEASES: THE BULGE-HELIX-BULGE MOTIF, NMR, 12 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRE-TRNA BULGE-HELIX-BULGE MOTIF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE MOLECULE WAS SYNTHESIZED IN VITRO BY T7 SOURCE 4 POLYMERASE RNA TRANSCRIPTION USING CHEMICALLY SYNTHESIZED DNA SOURCE 5 OLIGONUCLEOTIDES AS TEMPLATES KEYWDS ARCHAEAL BULGE-HELIX-BULGE MOTIF, PRE-TRNA SPLICING, ARCHAEA, RNA KEYWDS 2 STRUCTURE, RIBONUCLEIC ACID, RNA EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR J.L.DIENER,P.B.MOORE REVDAT 4 22-MAY-24 1A9L 1 REMARK REVDAT 3 16-FEB-22 1A9L 1 REMARK REVDAT 2 24-FEB-09 1A9L 1 VERSN REVDAT 1 17-JUN-98 1A9L 0 JRNL AUTH J.L.DIENER,P.B.MOORE JRNL TITL SOLUTION STRUCTURE OF A SUBSTRATE FOR THE ARCHAEAL PRE-TRNA JRNL TITL 2 SPLICING ENDONUCLEASES: THE BULGE-HELIX-BULGE MOTIF. JRNL REF MOL.CELL V. 1 883 1998 JRNL REFN ISSN 1097-2765 JRNL PMID 9660971 JRNL DOI 10.1016/S1097-2765(00)80087-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JOURNAL CITATION ABOVE. X-PLOR 3.851 ALSO WAS USED. REMARK 4 REMARK 4 1A9L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170563. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 303 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : NULL; NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : SEE JRNL REFERENCE REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; UNITYPLUS; OMEGA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; GE REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851, CNS REMARK 210 METHOD USED : TORSION ANGLE MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 65 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 A A 6 C4' - C3' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 G A 12 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 1 G A 12 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 A A 13 C4' - C3' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 A A 13 N9 - C1' - C2' ANGL. DEV. = 10.3 DEGREES REMARK 500 1 A A 13 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 A A 19 O3' - P - O5' ANGL. DEV. = 13.0 DEGREES REMARK 500 1 A A 21 N1 - C2 - N3 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 21 N9 - C4 - C5 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 G A 22 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 1 C A 25 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 30 N9 - C1' - C2' ANGL. DEV. = 8.2 DEGREES REMARK 500 2 A A 6 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 12 N9 - C1' - C2' ANGL. DEV. = 13.0 DEGREES REMARK 500 2 G A 12 O4' - C1' - N9 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 G A 12 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 2 A A 13 N9 - C1' - C2' ANGL. DEV. = 15.1 DEGREES REMARK 500 2 A A 13 O4' - C1' - N9 ANGL. DEV. = -7.7 DEGREES REMARK 500 2 A A 19 O3' - P - O5' ANGL. DEV. = 13.0 DEGREES REMARK 500 2 A A 19 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 A A 21 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES REMARK 500 2 A A 21 N1 - C2 - N3 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 A A 21 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 A A 21 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 G A 22 C1' - O4' - C4' ANGL. DEV. = 5.7 DEGREES REMARK 500 2 C A 25 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 U A 31 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 2 U A 31 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 C A 7 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 A A 11 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 3 G A 12 C5' - C4' - C3' ANGL. DEV. = 11.6 DEGREES REMARK 500 3 G A 12 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 3 G A 12 N9 - C1' - C2' ANGL. DEV. = 11.9 DEGREES REMARK 500 3 A A 13 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 3 A A 13 N9 - C1' - C2' ANGL. DEV. = 12.4 DEGREES REMARK 500 3 A A 13 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 3 A A 13 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 3 G A 14 N3 - C4 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 G A 22 C1' - O4' - C4' ANGL. DEV. = 5.7 DEGREES REMARK 500 3 C A 25 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 G A 26 C3' - C2' - C1' ANGL. DEV. = 7.2 DEGREES REMARK 500 3 U A 31 N1 - C1' - C2' ANGL. DEV. = 10.6 DEGREES REMARK 500 3 U A 31 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 4 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 A A 11 C3' - C2' - C1' ANGL. DEV. = -4.4 DEGREES REMARK 500 4 G A 12 C5' - C4' - C3' ANGL. DEV. = 12.7 DEGREES REMARK 500 4 G A 12 C5' - C4' - O4' ANGL. DEV. = 5.9 DEGREES REMARK 500 4 G A 12 N9 - C1' - C2' ANGL. DEV. = 10.3 DEGREES REMARK 500 4 A A 13 C4' - C3' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 4 A A 13 N9 - C1' - C2' ANGL. DEV. = 9.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 172 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 G A 3 0.06 SIDE CHAIN REMARK 500 1 G A 12 0.07 SIDE CHAIN REMARK 500 1 A A 13 0.12 SIDE CHAIN REMARK 500 1 G A 14 0.14 SIDE CHAIN REMARK 500 1 G A 18 0.17 SIDE CHAIN REMARK 500 1 A A 19 0.08 SIDE CHAIN REMARK 500 1 G A 22 0.06 SIDE CHAIN REMARK 500 1 A A 23 0.09 SIDE CHAIN REMARK 500 1 C A 24 0.07 SIDE CHAIN REMARK 500 1 C A 25 0.13 SIDE CHAIN REMARK 500 1 A A 28 0.08 SIDE CHAIN REMARK 500 1 A A 30 0.06 SIDE CHAIN REMARK 500 1 A A 32 0.11 SIDE CHAIN REMARK 500 1 U A 33 0.08 SIDE CHAIN REMARK 500 1 C A 34 0.09 SIDE CHAIN REMARK 500 1 A A 35 0.07 SIDE CHAIN REMARK 500 2 A A 13 0.18 SIDE CHAIN REMARK 500 2 G A 14 0.15 SIDE CHAIN REMARK 500 2 G A 15 0.09 SIDE CHAIN REMARK 500 2 U A 16 0.07 SIDE CHAIN REMARK 500 2 G A 18 0.19 SIDE CHAIN REMARK 500 2 A A 19 0.10 SIDE CHAIN REMARK 500 2 A A 23 0.08 SIDE CHAIN REMARK 500 2 C A 25 0.11 SIDE CHAIN REMARK 500 2 G A 27 0.07 SIDE CHAIN REMARK 500 2 U A 31 0.21 SIDE CHAIN REMARK 500 2 U A 33 0.07 SIDE CHAIN REMARK 500 3 G A 1 0.06 SIDE CHAIN REMARK 500 3 G A 12 0.06 SIDE CHAIN REMARK 500 3 A A 13 0.14 SIDE CHAIN REMARK 500 3 G A 14 0.19 SIDE CHAIN REMARK 500 3 G A 18 0.23 SIDE CHAIN REMARK 500 3 A A 19 0.06 SIDE CHAIN REMARK 500 3 A A 21 0.11 SIDE CHAIN REMARK 500 3 A A 23 0.07 SIDE CHAIN REMARK 500 3 C A 24 0.08 SIDE CHAIN REMARK 500 3 C A 25 0.11 SIDE CHAIN REMARK 500 3 G A 26 0.15 SIDE CHAIN REMARK 500 3 U A 31 0.14 SIDE CHAIN REMARK 500 3 A A 32 0.05 SIDE CHAIN REMARK 500 3 U A 33 0.08 SIDE CHAIN REMARK 500 3 C A 37 0.11 SIDE CHAIN REMARK 500 3 C A 38 0.09 SIDE CHAIN REMARK 500 4 C A 7 0.12 SIDE CHAIN REMARK 500 4 G A 12 0.09 SIDE CHAIN REMARK 500 4 A A 13 0.13 SIDE CHAIN REMARK 500 4 G A 14 0.17 SIDE CHAIN REMARK 500 4 G A 15 0.08 SIDE CHAIN REMARK 500 4 G A 18 0.18 SIDE CHAIN REMARK 500 4 A A 19 0.19 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 171 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2A9L RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE DBREF 1A9L A 1 38 PDB 1A9L 1A9L 1 38 SEQRES 1 A 38 G G G U G A C U C C A G A SEQRES 2 A 38 G G U C G A G A G A C C G SEQRES 3 A 38 G A G A U A U C A C C 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