HEADER RNA 18-JAN-05 1YKV TITLE CRYSTAL STRUCTURE OF THE DIELS-ALDER RIBOZYME COMPLEXED WITH THE TITLE 2 PRODUCT OF THE REACTION BETWEEN N-PENTYLMALEIMIDE AND COVALENTLY TITLE 3 ATTACHED 9-HYDROXYMETHYLANTHRACENE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIELS-ALDER RIBOZYME; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 11-MER; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DIELS-ALDER RIBOZYME; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: 38-MER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS RNA WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE WAS SOURCE 4 DERIVED FROM THE IN VITRO SELECTED RIBOZYME CATALYSING DIELS-ALDER SOURCE 5 REACTION BETWEEN THETHERED ANTHRACENE AND BIOTINYLATED MALEIMIDE; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 OTHER_DETAILS: THIS RNA WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE WAS SOURCE 9 DERIVED FROM THE IN VITRO SELECTED RIBOZYME CATALYSING DIELS-ALDER SOURCE 10 REACTION BETWEEN THETHERED ANTHRACENE AND BIOTINYLATED MALEIMIDE KEYWDS CARBON-CARBON BOND, CATALYTIC MECHANISM, DIELS-ALDER REACTION, KEYWDS 2 RIBOZYME, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.SERGANOV,S.KEIPER,L.MALININA,V.TERESHKO,E.SKRIPKIN,C.HOBARTNER, AUTHOR 2 A.POLONSKAIA,A.T.PHAN,R.WOMBACHER,R.MICURA,Z.DAUTER,A.JASCHKE, AUTHOR 3 D.J.PATEL REVDAT 5 23-AUG-23 1YKV 1 REMARK LINK REVDAT 4 13-JUL-11 1YKV 1 VERSN REVDAT 3 24-FEB-09 1YKV 1 VERSN REVDAT 2 22-MAR-05 1YKV 1 JRNL REVDAT 1 22-FEB-05 1YKV 0 JRNL AUTH A.SERGANOV,S.KEIPER,L.MALININA,V.TERESHKO,E.SKRIPKIN, JRNL AUTH 2 C.HOBARTNER,A.POLONSKAIA,A.T.PHAN,R.WOMBACHER,R.MICURA, JRNL AUTH 3 Z.DAUTER,A.JASCHKE,D.J.PATEL JRNL TITL STRUCTURAL BASIS FOR DIELS-ALDER RIBOZYME-CATALYZED JRNL TITL 2 CARBON-CARBON BOND FORMATION. JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 218 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 15723077 JRNL DOI 10.1038/NSMB906 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.9999 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 7522 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 388 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 568 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 2092 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.52000 REMARK 3 B22 (A**2) : -3.78000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.82000 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): 0.474 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.383 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 53.158 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.899 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2404 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 846 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3734 ; 1.480 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2200 ; 2.597 ; 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): 496 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1074 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 16 ; 0.009 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 593 ; 0.168 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1154 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 589 ; 0.115 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 46 ; 0.141 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.369 ; 0.200 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): 40 ; 0.206 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 11 ; 0.223 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.130 ; 0.200 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): 3432 ; 0.639 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3734 ; 0.599 ; 4.500 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 100 A 111 6 REMARK 3 1 C 100 C 111 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 376 ; 0.30 ; 5.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 376 ; 0.40 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 201 B 238 6 REMARK 3 1 D 201 D 238 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 2 B (A): 1122 ; 0.38 ; 5.00 REMARK 3 LOOSE THERMAL 2 B (A**2): 1122 ; 0.44 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 101 A 111 REMARK 3 ORIGIN FOR THE GROUP (A): 28.2942 25.6012 34.0195 REMARK 3 T TENSOR REMARK 3 T11: -0.0677 T22: -0.1984 REMARK 3 T33: -0.1962 T12: -0.0168 REMARK 3 T13: 0.2104 T23: 0.1709 REMARK 3 L TENSOR REMARK 3 L11: 6.6386 L22: 2.6940 REMARK 3 L33: 10.1018 L12: -0.1901 REMARK 3 L13: -7.8845 L23: -1.1824 REMARK 3 S TENSOR REMARK 3 S11: -0.0329 S12: 0.4567 S13: 0.3802 REMARK 3 S21: 0.1215 S22: 0.6192 S23: 0.4655 REMARK 3 S31: 0.0320 S32: -0.8974 S33: -0.5863 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 201 B 238 REMARK 3 ORIGIN FOR THE GROUP (A): 37.8218 26.7509 19.6474 REMARK 3 T TENSOR REMARK 3 T11: -0.2742 T22: -0.3025 REMARK 3 T33: -0.3375 T12: -0.1219 REMARK 3 T13: -0.0152 T23: 0.0803 REMARK 3 L TENSOR REMARK 3 L11: 1.0523 L22: 4.0371 REMARK 3 L33: 5.9779 L12: -0.4020 REMARK 3 L13: -1.3101 L23: 0.6861 REMARK 3 S TENSOR REMARK 3 S11: -0.0355 S12: 0.1519 S13: -0.0768 REMARK 3 S21: -0.4317 S22: 0.2839 S23: 0.3478 REMARK 3 S31: 0.2254 S32: -0.0508 S33: -0.2484 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 101 C 111 REMARK 3 ORIGIN FOR THE GROUP (A): 65.8600 34.2810 33.9042 REMARK 3 T TENSOR REMARK 3 T11: -0.0752 T22: -0.2747 REMARK 3 T33: 0.0883 T12: -0.0343 REMARK 3 T13: -0.2325 T23: -0.1567 REMARK 3 L TENSOR REMARK 3 L11: 10.1130 L22: 2.2998 REMARK 3 L33: 9.6968 L12: -0.6807 REMARK 3 L13: 8.4752 L23: 1.8477 REMARK 3 S TENSOR REMARK 3 S11: -0.1707 S12: 0.4862 S13: 0.2152 REMARK 3 S21: 0.1066 S22: 0.4069 S23: -0.5309 REMARK 3 S31: 0.1234 S32: 0.7441 S33: -0.2362 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 201 D 238 REMARK 3 ORIGIN FOR THE GROUP (A): 56.2401 33.4043 19.6050 REMARK 3 T TENSOR REMARK 3 T11: -0.2679 T22: -0.1949 REMARK 3 T33: -0.1198 T12: -0.1455 REMARK 3 T13: -0.0531 T23: -0.0477 REMARK 3 L TENSOR REMARK 3 L11: 1.2130 L22: 3.1080 REMARK 3 L33: 5.5759 L12: -1.6398 REMARK 3 L13: 1.9151 L23: -1.0809 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: 0.3928 S13: 0.1433 REMARK 3 S21: -0.3802 S22: 0.2310 S23: -0.5544 REMARK 3 S31: -0.0975 S32: 0.4293 S33: -0.2642 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1YKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031631. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : SI (111) DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR, BENT CYLINDRICAL REMARK 200 SI-MIRROR (RH COATING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8392 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.16200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: THE DIELS-ALDER RIBOZYME STRUCTURE FROM THE DIELS REMARK 200 -ALDER RIBOZYME-PRODUCT COMPLEX, PDB ENTRY 1YLS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, SODIUM HEPES, MAGNESIUM REMARK 280 CHLORIDE, ETHYLACETATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.01950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 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 B 230 O5' A B 230 C5' -0.062 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 G B 201 O4' - C4' - C3' ANGL. DEV. = -7.5 DEGREES REMARK 500 G B 201 C1' - O4' - C4' ANGL. DEV. = 5.7 DEGREES REMARK 500 G B 207 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 U B 222 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 U B 234 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 G D 201 O4' - C4' - C3' ANGL. DEV. = -8.1 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 B 246 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 213 OP1 REMARK 620 2 G D 213 OP1 80.9 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 B 240 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAI A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAI C 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YKQ RELATED DB: PDB REMARK 900 THE SAME RIBOZYME COMPLEXED WITH THE REACTION PRODUCT REMARK 900 RELATED ID: 1YLS RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE DAI HETGROUP IS CONNECTED TO THE 5' G OF THE REMARK 999 11-MER RNA VIA HEXAETHYLENEGLYCOL LINKER. THE REMARK 999 LINKER IS NOT VISIBLE IN THE ELECTRON DENSITY. DBREF 1YKV A 101 111 PDB 1YKV 1YKV 101 111 DBREF 1YKV B 201 238 PDB 1YKV 1YKV 201 238 DBREF 1YKV C 101 111 PDB 1YKV 1YKV 101 111 DBREF 1YKV D 201 238 PDB 1YKV 1YKV 201 238 SEQRES 1 A 11 G G A G C U C G C C C SEQRES 1 B 38 G G G C G A G G C C G U G SEQRES 2 B 38 C C A G C U C U U C G G A SEQRES 3 B 38 G C A A U A C U C G G C SEQRES 1 C 11 G G A G C U C G C C C SEQRES 1 D 38 G G G C G A G G C C G U G SEQRES 2 D 38 C C A G C U C U U C G G A SEQRES 3 D 38 G C A A U A C U C G G C HET DAI A 100 28 HET MG B 240 1 HET MG B 241 1 HET MG B 242 1 HET MG B 246 1 HET DAI C 100 28 HET MG D 340 1 HET MG D 341 1 HET MG D 342 1 HETNAM DAI (3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A- HETNAM 2 DAI TETRAHYDRO-4,9[1',2']-BENZENO-1H-BENZ[F]ISOINDOLE-1, HETNAM 3 DAI 3(2H)-DIONE HETNAM MG MAGNESIUM ION HETSYN DAI (11S,12S)-9-HYDROXYMETHYL-11,12-(2-PENTYL-1,3-DIOXO-2- HETSYN 2 DAI AZAPROPANO)-9,10-DIHYDRO-9,10-ETHANOANTHRACENE FORMUL 5 DAI 2(C24 H25 N O3) FORMUL 6 MG 7(MG 2+) LINK OP1 G B 213 MG MG B 246 1555 1555 2.14 LINK OP2 A B 216 MG MG B 242 1555 1555 2.07 LINK OP2 C B 233 MG MG B 241 1555 1555 2.17 LINK OP1 U B 234 MG MG B 240 1555 1555 2.27 LINK MG MG B 246 OP1 G D 213 1555 1555 2.03 LINK OP2 A D 216 MG MG D 342 1555 1555 2.11 LINK OP2 C D 233 MG MG D 341 1555 1555 2.15 LINK OP1 U D 234 MG MG D 340 1555 1555 2.16 SITE 1 AC1 1 U B 234 SITE 1 AC2 1 C B 233 SITE 1 AC3 2 A B 216 G B 217 SITE 1 AC4 2 G B 213 G D 213 SITE 1 AC5 1 U D 234 SITE 1 AC6 2 C D 210 C D 233 SITE 1 AC7 2 A D 216 G D 217 SITE 1 AC8 7 G A 102 A A 103 G B 213 C B 214 SITE 2 AC8 7 U B 231 A B 232 U B 234 SITE 1 AC9 8 U B 212 G C 102 A C 103 G D 213 SITE 2 AC9 8 C D 214 U D 231 A D 232 U D 234 CRYST1 78.288 44.039 79.998 90.00 106.87 90.00 P 1 21 1 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 0.012773 0.000000 0.003874 0.00000 SCALE2 0.000000 0.022707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013062 0.00000