HEADER RNA 27-JUN-05 2A43 TITLE CRYSTAL STRUCTURE OF A LUTEOVIRAL RNA PSEUDOKNOT AND MODEL FOR A TITLE 2 MINIMAL RIBOSOMAL FRAMESHIFTING MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED OLIGONUCLEOTIDE (RNA). THIS SOURCE 4 SEQUENCE IS A MUTATED FORM OF THAT NATURALLY FOUND IN POTATO SOURCE 5 LEAFROLL VIRUS KEYWDS PLRV, POTATO LEAF ROLL VIRUS; BWYV, BEET WESTERN YELLOW VIRUS, PK, KEYWDS 2 PSEUDOKNOT, RNA., RNA EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PALLAN,W.S.MARSHALL,J.HARP,F.C.JEWETT III,Z.WAWRZAK,B.A.BROWN II, AUTHOR 2 A.RICH,M.EGLI REVDAT 5 23-AUG-23 2A43 1 REMARK REVDAT 4 20-OCT-21 2A43 1 REMARK SEQADV LINK REVDAT 3 11-OCT-17 2A43 1 REMARK REVDAT 2 24-FEB-09 2A43 1 VERSN REVDAT 1 27-SEP-05 2A43 0 JRNL AUTH P.S.PALLAN,W.S.MARSHALL,J.HARP,F.C.JEWETT III,Z.WAWRZAK, JRNL AUTH 2 B.A.BROWN II,A.RICH,M.EGLI JRNL TITL CRYSTAL STRUCTURE OF A LUTEOVIRAL RNA PSEUDOKNOT AND MODEL JRNL TITL 2 FOR A MINIMAL RIBOSOMAL FRAMESHIFTING MOTIF JRNL REF BIOCHEMISTRY V. 44 11315 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 16114868 JRNL DOI 10.1021/BI051061I REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.114 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 905 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 18322 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 552 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 ANGLE DISTANCES (A) : 0.041 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : G. PARKINSON ET. AL., ACTA CRYST. REMARK 3 (1996) D52, 57-64. REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE WATERS 603, 686, 211, 584, 610, 666, 608 AND 638 HAVE PARTIAL REMARK 3 OCCUPANCIES. REMARK 3 THUS CLOSE CONTACTS BETWEEN THEM SHOULD BE IGNORED. REMARK 4 REMARK 4 2A43 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91980 REMARK 200 MONOCHROMATOR : SI MONOCHROMATOR REMARK 200 OPTICS : HORIZONTALLY FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19756 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 23.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 14.60 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.64 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.970 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, CCP4 (MOLREP) REMARK 200 STARTING MODEL: PDB ENTRY 437D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE, SODIUM REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291.0K 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 36.66667 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 18.33333 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 18.33333 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 36.66667 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 300 REMARK: ONE RNA PSEUDOKNOT PER ASYMMETRIC UNIT 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 514 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 610 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 684 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 686 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 690 LIES ON A SPECIAL POSITION. 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 G A 3 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 C A 4 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 C A 7 O5' - C5' - C4' ANGL. DEV. = -5.4 DEGREES REMARK 500 C A 7 N3 - C4 - C5 ANGL. DEV. = -5.7 DEGREES REMARK 500 C A 7 C4 - C5 - C6 ANGL. DEV. = 4.6 DEGREES REMARK 500 A A 8 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 A A 8 N1 - C2 - N3 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 8 C2 - N3 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 C A 9 C2 - N3 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 C A 14 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 C A 14 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES REMARK 500 C A 14 N3 - C4 - C5 ANGL. DEV. = -4.3 DEGREES REMARK 500 C A 16 C6 - N1 - C2 ANGL. DEV. = -3.5 DEGREES REMARK 500 A A 20 N1 - C2 - N3 ANGL. DEV. = 4.4 DEGREES REMARK 500 A A 21 N1 - C2 - N3 ANGL. DEV. = 3.2 DEGREES REMARK 500 A A 21 C2 - N3 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 24 N7 - C8 - N9 ANGL. DEV. = -4.0 DEGREES REMARK 500 A A 25 C8 - N9 - C4 ANGL. DEV. = 2.9 DEGREES 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 6 O6 REMARK 620 2 HOH A 202 O 175.1 REMARK 620 3 HOH A 203 O 86.4 91.5 REMARK 620 4 HOH A 204 O 80.0 96.3 105.6 REMARK 620 5 HOH A 205 O 94.1 89.0 166.1 88.1 REMARK 620 6 HOH A 206 O 99.1 85.1 84.3 169.9 81.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 207 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 208 O REMARK 620 2 HOH A 209 O 87.8 REMARK 620 3 HOH A 210 O 89.6 92.6 REMARK 620 4 HOH A 211 O 90.8 178.6 87.7 REMARK 620 5 HOH A 212 O 92.6 92.7 174.4 87.1 REMARK 620 6 HOH A 213 O 175.2 89.3 86.8 92.1 91.2 REMARK 620 7 HOH A 584 O 75.7 161.8 94.9 16.8 80.6 107.7 REMARK 620 N 1 2 3 4 5 6 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 207 DBREF 2A43 A 3 28 GB 23953793 AY138970 1676 1701 SEQADV 2A43 U A 17 GB 23953793 C 1690 ENGINEERED MUTATION SEQADV 2A43 C A 18 GB 23953793 A 1691 ENGINEERED MUTATION SEQRES 1 A 26 G C G G C A C C G U C C G SEQRES 2 A 26 C U C A A A C A A A C G G HET MG A 201 1 HET MG A 207 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 2(MG 2+) FORMUL 4 HOH *201(H2 O) LINK O6 G A 6 MG MG A 201 1555 1555 2.37 LINK MG MG A 201 O HOH A 202 1555 1555 2.13 LINK MG MG A 201 O HOH A 203 1555 1555 2.27 LINK MG MG A 201 O HOH A 204 1555 1555 2.09 LINK MG MG A 201 O HOH A 205 1555 1555 2.30 LINK MG MG A 201 O HOH A 206 1555 1555 2.24 LINK MG MG A 207 O HOH A 208 1555 1555 2.10 LINK MG MG A 207 O HOH A 209 1555 1555 2.09 LINK MG MG A 207 O HOH A 210 1555 1555 2.16 LINK MG MG A 207 O HOH A 211 1555 1555 2.10 LINK MG MG A 207 O HOH A 212 1555 1555 2.19 LINK MG MG A 207 O HOH A 213 1555 1555 2.18 LINK MG MG A 207 O HOH A 584 1555 1555 3.12 SITE 1 AC1 6 G A 6 HOH A 202 HOH A 203 HOH A 204 SITE 2 AC1 6 HOH A 205 HOH A 206 SITE 1 AC2 6 HOH A 208 HOH A 209 HOH A 210 HOH A 211 SITE 2 AC2 6 HOH A 212 HOH A 213 CRYST1 53.250 53.250 55.000 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 0.018779 0.010842 0.000000 0.00000 SCALE2 0.000000 0.021685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018182 0.00000