HEADER RNA 11-OCT-19 6T3S TITLE STRUCTURE OF OCEANOBACILLUS IHEYENSIS GROUP II INTRON U-MUTANT TITLE 2 (C289U/C358U/G385A) IN THE PRESENCE OF NA+, MG2+ AND 5'-EXON COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROUP IIC INTRON RIBOZYME; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAINS 1-5 AND 5'-EXON; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: OCEANOBACILLUS IHEYENSIS; SOURCE 4 ORGANISM_TAXID: 182710; SOURCE 5 OTHER_DETAILS: IN VITRO TRANSCRIPTION SYSTEM KEYWDS RIBOZYME, SELF-SPLICING, RETROTRANSPOSITION, SPLICEOSOME, RNA EXPDTA X-RAY DIFFRACTION AUTHOR M.MARCIA,A.M.PYLE REVDAT 3 24-JAN-24 6T3S 1 LINK REVDAT 2 17-JUN-20 6T3S 1 JRNL REVDAT 1 13-MAY-20 6T3S 0 JRNL AUTH J.MANIGRASSO,I.CHILLON,V.GENNA,P.VIDOSSICH,S.SOMAROWTHU, JRNL AUTH 2 A.M.PYLE,M.DE VIVO,M.MARCIA JRNL TITL VISUALIZING GROUP II INTRON DYNAMICS BETWEEN THE FIRST AND JRNL TITL 2 SECOND STEPS OF SPLICING. JRNL REF NAT COMMUN V. 11 2837 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32503992 JRNL DOI 10.1038/S41467-020-16741-4 REMARK 2 REMARK 2 RESOLUTION. 3.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 29194 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1550 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) : 3.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2112 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 8390 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 132.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.69000 REMARK 3 B22 (A**2) : -4.61000 REMARK 3 B33 (A**2) : 1.92000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.414 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.332 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 42.364 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 9457 ; 0.008 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 3863 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 14742 ; 1.792 ; 1.283 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9399 ; 1.660 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1570 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4707 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 2082 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -4 A 390 REMARK 3 ORIGIN FOR THE GROUP (A): -24.5180 8.5500 -25.6190 REMARK 3 T TENSOR REMARK 3 T11: 0.4552 T22: 0.4017 REMARK 3 T33: 0.3487 T12: 0.0170 REMARK 3 T13: 0.0563 T23: 0.0292 REMARK 3 L TENSOR REMARK 3 L11: 0.7941 L22: 2.2587 REMARK 3 L33: 1.2313 L12: 0.9353 REMARK 3 L13: -0.8267 L23: -0.7965 REMARK 3 S TENSOR REMARK 3 S11: -0.2577 S12: 0.3139 S13: -0.1398 REMARK 3 S21: -0.8762 S22: 0.1607 S23: -0.2034 REMARK 3 S31: 0.1962 S32: -0.0958 S33: 0.0970 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 6T3S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292104801. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-13 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979500 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(220) SIDE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION MARCH 30, 2013 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30804 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.279 REMARK 200 RESOLUTION RANGE LOW (A) : 48.893 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.99500 REMARK 200 R SYM FOR SHELL (I) : 0.99500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.5 REMARK 200 STARTING MODEL: 4FAX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA-HEPES PH 7.0, 100 MM REMARK 280 MAGNESIUM ACETATE, 150 MM SODIUM CHLORIDE, 4% PEG 8000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 44.94500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 113.94800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.62000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 113.94800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.94500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.62000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -232.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 G A -7 REMARK 465 G A -6 REMARK 465 G A -5 REMARK 465 G A 1 REMARK 465 A A 183 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 A A 181 C8 N7 C5 C6 N6 N1 C2 REMARK 470 A A 181 N3 C4 REMARK 470 A A 184 N9 C8 N7 C5 C6 N6 N1 REMARK 470 A A 184 C2 N3 C4 REMARK 470 A A 207 N9 C8 N7 C5 C6 N6 N1 REMARK 470 A A 207 C2 N3 C4 REMARK 470 A A 223 C8 N7 C5 C6 N6 N1 C2 REMARK 470 A A 223 N3 C4 REMARK 470 G A 390 O5' C5' C4' O4' C3' O3' C2' REMARK 470 G A 390 O2' C1' N9 C8 N7 C5 C6 REMARK 470 G A 390 O6 N1 C2 N2 N3 C4 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 NA NA A 427 O HOH A 520 1.66 REMARK 500 O2' A A 35 OP2 U A 37 2.09 REMARK 500 O2' A A 222 OP2 A A 224 2.11 REMARK 500 N7 G A 160 N2 G A 218 2.15 REMARK 500 O6 G A 275 O HOH A 501 2.17 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 A A 49 O3' A A 50 P -0.080 REMARK 500 A A 245 O3' A A 246 P -0.084 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 C A 44 O5' - P - OP2 ANGL. DEV. = 7.6 DEGREES REMARK 500 G A 58 O5' - P - OP2 ANGL. DEV. = -5.8 DEGREES REMARK 500 U A 59 C3' - C2' - O2' ANGL. DEV. = -17.9 DEGREES REMARK 500 G A 68 O5' - P - OP1 ANGL. DEV. = -6.0 DEGREES REMARK 500 C A 119 O5' - P - OP2 ANGL. DEV. = -7.8 DEGREES REMARK 500 A A 174 O5' - P - OP1 ANGL. DEV. = 12.1 DEGREES REMARK 500 A A 174 O5' - P - OP2 ANGL. DEV. = -8.3 DEGREES REMARK 500 A A 181 O5' - P - OP1 ANGL. DEV. = 10.6 DEGREES REMARK 500 U A 195 O5' - P - OP2 ANGL. DEV. = -6.5 DEGREES REMARK 500 U A 198 O5' - P - OP2 ANGL. DEV. = -5.7 DEGREES REMARK 500 A A 223 C2' - C3' - O3' ANGL. DEV. = 11.2 DEGREES REMARK 500 A A 240 O5' - P - OP1 ANGL. DEV. = -5.5 DEGREES REMARK 500 A A 241 O5' - P - OP1 ANGL. DEV. = 9.1 DEGREES REMARK 500 A A 241 O5' - P - OP2 ANGL. DEV. = -8.1 DEGREES REMARK 500 G A 242 O5' - P - OP1 ANGL. DEV. = 9.5 DEGREES REMARK 500 G A 242 O5' - P - OP2 ANGL. DEV. = -5.7 DEGREES REMARK 500 A A 247 O5' - P - OP2 ANGL. DEV. = -6.0 DEGREES REMARK 500 A A 276 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 G A 284 O5' - P - OP1 ANGL. DEV. = 8.6 DEGREES REMARK 500 A A 287 C4' - C3' - O3' ANGL. DEV. = 14.4 DEGREES REMARK 500 G A 288 O5' - P - OP2 ANGL. DEV. = -6.5 DEGREES REMARK 500 A A 297 C4' - C3' - O3' ANGL. DEV. = 12.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 EPE A 428 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 420 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 0 O3' REMARK 620 2 U A 0 O2' 69.3 REMARK 620 3 U A 375 OP1 80.9 91.6 REMARK 620 4 C A 377 OP2 91.9 160.5 90.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 408 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 66 OP2 REMARK 620 2 A A 67 OP1 86.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 413 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 67 OP2 REMARK 620 2 G A 68 N7 76.5 REMARK 620 3 HOH A 504 O 67.5 77.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 119 OP1 REMARK 620 2 G A 239 OP1 152.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 410 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 154 OP2 REMARK 620 2 G A 155 N7 74.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 324 O6 REMARK 620 2 G A 325 O6 64.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 421 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 358 OP2 REMARK 620 2 C A 377 OP1 75.8 REMARK 620 N 1 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 423 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 424 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 425 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 426 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 427 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 428 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AF4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 431 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6T3K RELATED DB: PDB REMARK 900 6T3K CONTAINS A DIFFERENT MUTANT OF THE SAME RNA (G-MUTANT, C289G/ REMARK 900 C358G/G385C) CRYSTALLIZED IN THE PRESENCE OF K+, MG2+ AND 5'-EXON REMARK 900 RELATED ID: 6T3N RELATED DB: PDB REMARK 900 6T3N CONTAINS A DIFFERENT MUTANT OF THE SAME RNA (G-MUTANT, C289G/ REMARK 900 C358G/G385C) CRYSTALLIZED IN THE PRESENCE OF NA+, MG2+ AND 5'-EXON REMARK 900 RELATED ID: 6T3R RELATED DB: PDB REMARK 900 6T3R CONTAINS THE SAME RNA CRYSTALLIZED IN THE PRESENCE OF K+, MG2+ REMARK 900 AND 5'-EXON DBREF 6T3S A -7 390 PDB 6T3S 6T3S -7 390 SEQRES 1 A 398 G G G G U U A U G U G U G SEQRES 2 A 398 C C C G G C A U G G G U G SEQRES 3 A 398 C A G U C U A U A G G G U SEQRES 4 A 398 G A G A G U C C C G A A C SEQRES 5 A 398 U G U G A A G G C A G A A SEQRES 6 A 398 G U A A C A G U U A G C C SEQRES 7 A 398 U A A C G C A A G G G U G SEQRES 8 A 398 U C C G U G G C G A C A U SEQRES 9 A 398 G G A A U C U G A A G G A SEQRES 10 A 398 A G C G G A C G G C A A A SEQRES 11 A 398 C C U U C G G U C U G A G SEQRES 12 A 398 G A A C A C G A A C U U C SEQRES 13 A 398 A U A U G A G G C U A G G SEQRES 14 A 398 U A U C A A U G G A U G A SEQRES 15 A 398 G U U U G C A U A A C A A SEQRES 16 A 398 A A C A A A G U C C U U U SEQRES 17 A 398 C U G C C A A A G U U G G SEQRES 18 A 398 U A C A G A G U A A A U G SEQRES 19 A 398 A A G C A G A U U G A U G SEQRES 20 A 398 A A G G G A A A G A C U G SEQRES 21 A 398 C A U U C U U A C C C G G SEQRES 22 A 398 G G A G G U C U G G A A A SEQRES 23 A 398 C A G A A G U C A G U A G SEQRES 24 A 398 A A G U C A U A G U A C C SEQRES 25 A 398 C U G U U C G C A G G G G SEQRES 26 A 398 A A G G A C G G A A C A A SEQRES 27 A 398 G U A U G G C G U U C G C SEQRES 28 A 398 G C C U A A G C U U G A A SEQRES 29 A 398 C U G C C G U A U A C C G SEQRES 30 A 398 A A C G G U A C G U A C G SEQRES 31 A 398 G U A G U G U G HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET MG A 405 1 HET MG A 406 1 HET MG A 407 1 HET MG A 408 1 HET MG A 409 1 HET MG A 410 1 HET MG A 411 1 HET MG A 412 1 HET MG A 413 1 HET MG A 414 1 HET MG A 415 1 HET MG A 416 1 HET MG A 417 1 HET MG A 418 1 HET MG A 419 1 HET MG A 420 1 HET NA A 421 1 HET NA A 422 1 HET NA A 423 1 HET NA A 424 1 HET NA A 425 1 HET NA A 426 1 HET NA A 427 1 HET EPE A 428 5 HET NA A 429 1 HET EPE A 430 15 HET EPE A 431 15 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 MG 20(MG 2+) FORMUL 22 NA 8(NA 1+) FORMUL 29 EPE 3(C8 H18 N2 O4 S) FORMUL 33 HOH *25(H2 O) LINK O3' U A 0 MG MG A 420 1555 1555 2.57 LINK O2' U A 0 MG MG A 420 1555 1555 1.91 LINK OP1 C A 6 MG MG A 411 1555 1555 1.95 LINK O6 G A 28 NA NA A 424 1555 1555 2.78 LINK O6 G A 46 MG MG A 402 1555 1555 3.00 LINK OP2 U A 66 MG MG A 408 1555 1555 2.11 LINK OP1 A A 67 MG MG A 408 1555 1555 2.42 LINK OP2 A A 67 MG MG A 413 1555 1555 2.26 LINK N7 G A 68 MG MG A 413 1555 1555 2.46 LINK OP1 A A 105 MG MG A 407 1555 1555 2.32 LINK OP1 G A 107 MG MG A 403 1555 1555 2.35 LINK OP1 C A 119 MG MG A 406 1555 1555 2.16 LINK OP2 G A 136 MG MG A 418 1555 1555 2.29 LINK N7 G A 142 MG MG A 417 1555 1555 2.31 LINK OP2 C A 145 MG MG A 419 1555 1555 2.80 LINK OP2 A A 154 MG MG A 410 1555 1555 2.00 LINK N7 G A 155 MG MG A 410 1555 1555 2.51 LINK OP1 G A 169 MG MG A 412 1555 1555 2.05 LINK O6 G A 194 NA NA A 426 1555 1555 2.85 LINK OP1 G A 239 MG MG A 406 1555 1555 1.89 LINK O6 G A 266 NA NA A 429 1555 1555 3.08 LINK OP2 G A 269 NA NA A 427 1555 1555 2.08 LINK OP2 A A 283 MG MG A 416 1555 1555 2.47 LINK OP1 U A 285 MG MG A 414 1555 1555 2.55 LINK OP2 G A 320 NA NA A 422 1555 1555 2.67 LINK O6 G A 324 MG MG A 401 1555 1555 2.94 LINK O6 G A 325 MG MG A 401 1555 1555 2.47 LINK OP2 U A 358 NA NA A 421 1555 1555 2.41 LINK OP2 C A 372 MG MG A 404 1555 1555 2.03 LINK OP1 U A 375 MG MG A 420 1555 1555 2.19 LINK OP2 C A 377 MG MG A 420 1555 1555 2.06 LINK OP1 C A 377 NA NA A 421 1555 1555 2.80 LINK MG MG A 413 O HOH A 504 1555 1555 2.08 LINK NA NA A 423 O HOH A 524 1555 1555 2.28 SITE 1 AC1 2 G A 324 G A 325 SITE 1 AC2 1 G A 46 SITE 1 AC3 1 G A 107 SITE 1 AC4 1 C A 372 SITE 1 AC5 1 U A 379 SITE 1 AC6 3 C A 119 A A 174 G A 239 SITE 1 AC7 1 A A 105 SITE 1 AC8 2 U A 66 A A 67 SITE 1 AC9 1 G A 284 SITE 1 AD1 2 A A 154 G A 155 SITE 1 AD2 1 C A 6 SITE 1 AD3 1 G A 169 SITE 1 AD4 3 A A 67 G A 68 HOH A 504 SITE 1 AD5 1 U A 285 SITE 1 AD6 1 C A 377 SITE 1 AD7 1 A A 283 SITE 1 AD8 1 G A 142 SITE 1 AD9 2 G A 136 U A 225 SITE 1 AE1 1 C A 145 SITE 1 AE2 3 U A 0 U A 375 C A 377 SITE 1 AE3 3 U A 289 U A 358 C A 377 SITE 1 AE4 1 G A 320 SITE 1 AE5 2 G A 15 HOH A 524 SITE 1 AE6 2 A A 27 G A 28 SITE 1 AE7 1 G A 264 SITE 1 AE8 2 G A 194 U A 195 SITE 1 AE9 2 G A 269 HOH A 520 SITE 1 AF1 3 A A 115 C A 116 G A 117 SITE 1 AF2 1 G A 266 SITE 1 AF3 5 C A 38 C A 39 G A 242 G A 243 SITE 2 AF3 5 G A 244 SITE 1 AF4 5 G A 79 G A 80 U A 82 G A 97 SITE 2 AF4 5 G A 98 CRYST1 89.890 95.240 227.896 90.00 90.00 90.00 P 21 21 21 4 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 0.011125 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010500 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004388 0.00000