HEADER RNA 13-OCT-98 3PHP TITLE STRUCTURE OF THE 3' HAIRPIN OF THE TYMV PSEUDOKNOT: PREFORMATION IN TITLE 2 RNA FOLDING COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*GP*UP*UP*CP*CP*GP*AP*GP*GP*GP*UP*CP*AP*UP*CP*GP*GP*AP*AP*CP*CP* COMPND 4 A) -3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS CHEMICALLY SYNTHESIZED FROM TURNIP YELLOW SOURCE 4 MOSAIC VIRUS KEYWDS RNA, PSEUDOKNOT, TYMV, RIBONUCLEIC ACID EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.H.KOLK,M.VAN DER GRAAF,S.S.WIJMENGA,C.W.A.PLEIJ,H.A.HEUS, AUTHOR 2 C.W.HILBERS REVDAT 6 27-DEC-23 3PHP 1 REMARK REVDAT 5 16-MAR-22 3PHP 1 REMARK REVDAT 4 24-FEB-09 3PHP 1 VERSN REVDAT 3 01-APR-03 3PHP 1 JRNL REVDAT 2 22-DEC-99 3PHP 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 21-OCT-98 3PHP 0 JRNL AUTH M.H.KOLK,M.VAN DER GRAAF,C.T.FRANSEN,S.S.WIJMENGA,C.W.PLEIJ, JRNL AUTH 2 H.A.HEUS,C.W.HILBERS JRNL TITL STRUCTURE OF THE 3'-HAIRPIN OF THE TYMV PSEUDOKNOT: JRNL TITL 2 PREFORMATION IN RNA FOLDING. JRNL REF EMBO J. V. 17 7498 1998 JRNL REFN ISSN 0261-4189 JRNL PMID 9857204 JRNL DOI 10.1093/EMBOJ/17.24.7498 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PHP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008059. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : JR-)NOESY; DQF COSY; {31P-1H} REMARK 210 HETCOR; {13C-1H} HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AM; AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 REMARK 210 REMARK 210 REMARK: IONIC_STRENGTH: 20 MM SODIUM PHOSPHATE PRESSURE: 1 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 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. = -3.2 DEGREES REMARK 500 1 G A 2 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 1 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.5 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. = -3.0 DEGREES REMARK 500 1 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 G A 7 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 G A 7 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 8 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 9 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 10 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 G A 11 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 U A 12 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 1 C A 13 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 17 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 17 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 G A 18 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 G A 18 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 19 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 A A 19 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 A A 19 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 20 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 C A 21 C3' - C2' - C1' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 C A 21 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 A A 23 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 23 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 G A 2 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 2 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 G A 7 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 7 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 G A 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 8 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 9 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 341 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 1 0.05 SIDE CHAIN REMARK 500 2 G A 1 0.05 SIDE CHAIN REMARK 500 2 C A 16 0.06 SIDE CHAIN REMARK 500 3 G A 1 0.05 SIDE CHAIN REMARK 500 4 G A 1 0.05 SIDE CHAIN REMARK 500 4 C A 5 0.06 SIDE CHAIN REMARK 500 4 C A 16 0.06 SIDE CHAIN REMARK 500 4 A A 20 0.05 SIDE CHAIN REMARK 500 5 G A 1 0.05 SIDE CHAIN REMARK 500 5 C A 16 0.06 SIDE CHAIN REMARK 500 6 G A 1 0.05 SIDE CHAIN REMARK 500 7 G A 1 0.05 SIDE CHAIN REMARK 500 8 G A 1 0.05 SIDE CHAIN REMARK 500 9 G A 1 0.05 SIDE CHAIN REMARK 500 10 G A 1 0.05 SIDE CHAIN REMARK 500 10 C A 16 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 3PHP A 1 23 PDB 3PHP 3PHP 1 23 SEQRES 1 A 23 G G U U C C G A G G G U C SEQRES 2 A 23 A U C G G A A C C A 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