HEADER RNA 15-MAR-97 1AFX TITLE UGAA EUKARYOTIC RIBOSOMAL RNA TETRALOOP, NMR, 13 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*UP*GP*UP*GP*AP*AP*CP*AP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UGA; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CONSERVED UGAA TETRALOOP FROM EUKARYOTIC 16S-LIKE COMPND 7 RIBOSOMAL RNA (5'-R(GGUGUGAACACC)-3') SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RIBONUCLEIC ACID, TETRALOOP, RIBOSOMAL RNA, RNA EXPDTA SOLUTION NMR NUMMDL 13 AUTHOR S.E.BUTCHER,T.DIECKMANN,J.FEIGON REVDAT 5 22-MAY-24 1AFX 1 REMARK REVDAT 4 16-FEB-22 1AFX 1 REMARK REVDAT 3 24-FEB-09 1AFX 1 VERSN REVDAT 2 01-APR-03 1AFX 1 JRNL REVDAT 1 15-MAY-97 1AFX 0 JRNL AUTH S.E.BUTCHER,F.H.ALLAIN,J.FEIGON JRNL TITL SOLUTION STRUCTURE OF THE LOOP B DOMAIN FROM THE HAIRPIN JRNL TITL 2 RIBOZYME. JRNL REF NAT.STRUCT.BIOL. V. 6 212 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10074938 JRNL DOI 10.1038/6651 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1AFX 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_1000170766. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR 3.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 13 REMARK 210 CONFORMERS, SELECTION CRITERIA : CLUSTER OF 13 STRUCTURES WITH REMARK 210 COMMON FOLD 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 HO2' C A 9 O5' A A 10 1.40 REMARK 500 H2' U A 3 O4' G A 4 1.49 REMARK 500 HO2' G A 6 O5' A A 7 1.50 REMARK 500 HO2' G A 2 O5' U A 3 1.56 REMARK 500 HO2' A A 8 OP2 C A 9 1.57 REMARK 500 HO2' A A 7 O5' A A 8 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 11 G A 6 C8 G A 6 N9 -0.046 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 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 G A 2 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 G A 2 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 G A 4 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 4 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 G A 4 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 G A 6 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 A A 7 C5 - N7 - C8 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 A A 7 N7 - C8 - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 A A 7 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 8 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 A A 8 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 A A 8 N7 - C8 - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 A A 8 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 A A 10 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 A A 10 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 G A 1 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 G A 2 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 G A 4 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 G A 4 N7 - C8 - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 G A 4 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 G A 6 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 G A 6 N7 - C8 - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 2 G A 6 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 A A 7 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 A A 7 N7 - C8 - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 A A 7 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 A A 8 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 A A 8 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 A A 8 N7 - C8 - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 2 A A 8 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 A A 10 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 A A 10 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 A A 10 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 G A 1 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 318 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 8 C A 9 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1AFX A 1 12 PDB 1AFX 1AFX 1 12 SEQRES 1 A 12 G G U G U G A A C A 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