HEADER RNA 24-NOV-98 437D TITLE CRYSTAL STRUCTURE OF AN RNA PSEUDOKNOT FROM BEET WESTERN YELLOW VIRUS TITLE 2 INVOLVED IN RIBOSOMAL FRAMESHIFTING COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA SEQUENCE TAKEN FROM BEET WESTERN YELLOW VIRUS KEYWDS PSEUDOKNOT, RNA, TRIPLEX, VIRAL FRAMESHIFTING EXPDTA X-RAY DIFFRACTION AUTHOR L.SU,L.CHEN,M.EGLI,J.M.BERGER,A.RICH REVDAT 5 28-FEB-24 437D 1 REMARK LINK REVDAT 4 16-NOV-11 437D 1 VERSN HETATM REVDAT 3 24-FEB-09 437D 1 VERSN REVDAT 2 19-FEB-99 437D 1 REVDAT 1 03-DEC-98 437D 0 JRNL AUTH L.SU,L.CHEN,M.EGLI,J.M.BERGER,A.RICH JRNL TITL MINOR GROOVE RNA TRIPLEX IN THE CRYSTAL STRUCTURE OF A JRNL TITL 2 RIBOSOMAL FRAMESHIFTING VIRAL PSEUDOKNOT. JRNL REF NAT.STRUCT.BIOL. V. 6 285 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10074948 JRNL DOI 10.1038/6722 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.0 REMARK 3 NUMBER OF REFLECTIONS : 7877 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 916 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 614 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.45600 REMARK 3 B22 (A**2) : -2.45600 REMARK 3 B33 (A**2) : 4.91100 REMARK 3 B12 (A**2) : -0.28200 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.870 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 437D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000179231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1406 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8793 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.16500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.38667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.69333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.69333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 93.38667 REMARK 290 REMARK 290 REMARK: NULL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 118 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 122 LIES ON A SPECIAL POSITION. 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 C A 14 0.08 SIDE CHAIN REMARK 500 G A 27 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 100 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP A 1 O2B REMARK 620 2 GTP A 1 O3G 96.0 REMARK 620 3 G A 2 OP1 83.7 176.3 REMARK 620 4 HOH A 170 O 111.2 88.8 94.8 REMARK 620 5 HOH A 183 O 81.4 88.8 87.5 167.3 REMARK 620 6 HOH A 232 O 161.7 95.6 83.9 83.1 84.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 16 O2' REMARK 620 2 G A 16 N3 94.2 REMARK 620 3 A A 21 OP2 171.6 92.7 REMARK 620 4 A A 21 N7 64.5 152.1 107.4 REMARK 620 5 HOH A 149 O 71.3 99.4 112.2 90.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 101 DBREF 437D A 1 28 PDB 437D 437D 1 28 SEQRES 1 A 28 GTP G C G C G G C A C C G U SEQRES 2 A 28 C C G C G G A A C A A A C SEQRES 3 A 28 G G MODRES 437D GTP A 1 G GUANOSINE-5'-TRIPHOSPHATE HET GTP A 1 32 HET MG A 100 1 HET NA A 101 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 MG MG 2+ FORMUL 3 NA NA 1+ FORMUL 4 HOH *124(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.57 LINK O2B GTP A 1 MG MG A 100 1555 1555 2.02 LINK O3G GTP A 1 MG MG A 100 1555 1555 2.07 LINK OP1 G A 2 MG MG A 100 1555 1555 2.07 LINK O2' G A 16 NA NA A 101 1555 1555 2.81 LINK N3 G A 16 NA NA A 101 1555 1555 2.77 LINK OP2 A A 21 NA NA A 101 1555 1555 2.60 LINK N7 A A 21 NA NA A 101 1555 1555 2.91 LINK MG MG A 100 O HOH A 170 1555 1555 2.21 LINK MG MG A 100 O HOH A 183 1555 1555 2.25 LINK MG MG A 100 O HOH A 232 1555 1555 2.08 LINK NA NA A 101 O HOH A 149 1555 1555 2.77 SITE 1 AC1 5 GTP A 1 G A 2 HOH A 170 HOH A 183 SITE 2 AC1 5 HOH A 232 SITE 1 AC2 4 G A 16 C A 17 A A 21 HOH A 149 CRYST1 30.080 30.080 140.080 90.00 90.00 120.00 P 32 2 1 6 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 0.033245 0.019194 0.000000 0.00000 SCALE2 0.000000 0.038388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007139 0.00000 HETATM 1 PG GTP A 1 21.822 31.994 29.109 1.00 49.92 P HETATM 2 O1G GTP A 1 21.871 30.599 29.788 1.00 49.92 O HETATM 3 O2G GTP A 1 22.670 33.021 29.910 1.00 49.92 O HETATM 4 O3G GTP A 1 20.381 32.538 29.074 1.00 49.83 O HETATM 5 O3B GTP A 1 22.380 31.790 27.538 1.00 35.56 O HETATM 6 PB GTP A 1 21.759 30.909 26.280 1.00 37.70 P HETATM 7 O1B GTP A 1 22.474 29.645 26.102 1.00 29.35 O HETATM 8 O2B GTP A 1 20.257 30.866 26.540 1.00 47.32 O HETATM 9 O3A GTP A 1 21.974 31.768 25.001 1.00 42.13 O HETATM 10 PA GTP A 1 21.154 32.859 24.257 1.00 39.67 P HETATM 11 O1A GTP A 1 21.895 33.306 23.028 1.00 44.13 O HETATM 12 O2A GTP A 1 20.621 33.855 25.178 1.00 31.03 O HETATM 13 O5' GTP A 1 19.993 31.892 23.655 1.00 37.83 O HETATM 14 C5' GTP A 1 18.850 32.400 22.985 1.00 35.82 C HETATM 15 C4' GTP A 1 18.034 31.231 22.492 1.00 30.22 C HETATM 16 O4' GTP A 1 18.794 30.524 21.488 1.00 21.83 O HETATM 17 C3' GTP A 1 17.791 30.216 23.599 1.00 25.18 C HETATM 18 O3' GTP A 1 16.570 30.526 24.241 1.00 26.43 O HETATM 19 C2' GTP A 1 17.625 28.922 22.820 1.00 20.09 C HETATM 20 O2' GTP A 1 16.324 28.911 22.253 1.00 24.35 O HETATM 21 C1' GTP A 1 18.605 29.133 21.658 1.00 19.45 C HETATM 22 N9 GTP A 1 19.906 28.508 21.848 1.00 23.58 N HETATM 23 C8 GTP A 1 21.083 29.124 22.233 1.00 20.55 C HETATM 24 N7 GTP A 1 22.108 28.298 22.269 1.00 28.46 N HETATM 25 C5 GTP A 1 21.570 27.074 21.891 1.00 20.33 C HETATM 26 C6 GTP A 1 22.162 25.824 21.704 1.00 29.07 C HETATM 27 O6 GTP A 1 23.340 25.505 21.887 1.00 45.12 O HETATM 28 N1 GTP A 1 21.245 24.875 21.269 1.00 34.15 N HETATM 29 C2 GTP A 1 19.901 25.096 21.073 1.00 27.53 C HETATM 30 N2 GTP A 1 19.185 24.088 20.662 1.00 26.93 N HETATM 31 N3 GTP A 1 19.324 26.240 21.274 1.00 21.79 N HETATM 32 C4 GTP A 1 20.194 27.193 21.659 1.00 15.79 C