HEADER RNA 17-DEC-25 21LD TITLE CRYSTAL STRUCTURE OF THE ESTER-HYDROLYZING RIBOZYME (EHR) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*CP*AP*CP*UP*GP*CP*GP*AP*GP*UP*UP*UP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'- COMPND 7 R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP* COMPND 8 CP*C)-3'); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'- COMPND 13 R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP* COMPND 14 UP*G)-3'); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS RIBOZYME, ESTER HYDROLYSIS, RNA, GUANINE EXPDTA X-RAY DIFFRACTION AUTHOR Y.HE,L.HUANG REVDAT 1 04-NOV-26 21LD 0 JRNL AUTH Y.HE,L.HUANG JRNL TITL CRYSTAL STRUCTURE OF THE ESTER-HYDROLYZING RIBOZYME (EHR) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 6147 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 293 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.9400 - 3.3900 0.93 2899 142 0.1497 0.1710 REMARK 3 2 3.3900 - 2.6900 1.00 2955 151 0.3079 0.3120 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.318 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.791 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 94.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1473 REMARK 3 ANGLE : 0.937 2288 REMARK 3 CHIRALITY : 0.122 307 REMARK 3 PLANARITY : 0.002 63 REMARK 3 DIHEDRAL : 11.112 732 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5053 -18.3549 1.9889 REMARK 3 T TENSOR REMARK 3 T11: 0.9588 T22: 0.9190 REMARK 3 T33: 0.9780 T12: -0.1329 REMARK 3 T13: 0.0389 T23: -0.1449 REMARK 3 L TENSOR REMARK 3 L11: 3.5701 L22: 4.1426 REMARK 3 L33: 1.1907 L12: -1.5084 REMARK 3 L13: -0.6837 L23: 2.2441 REMARK 3 S TENSOR REMARK 3 S11: 0.4275 S12: -0.1535 S13: 0.1639 REMARK 3 S21: -0.1984 S22: -0.6914 S23: 0.5552 REMARK 3 S31: -0.3995 S32: -0.4253 S33: 0.0221 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.3483 -12.3845 5.4858 REMARK 3 T TENSOR REMARK 3 T11: 0.7944 T22: 0.8884 REMARK 3 T33: 0.9813 T12: -0.1040 REMARK 3 T13: -0.0428 T23: -0.1388 REMARK 3 L TENSOR REMARK 3 L11: 6.0782 L22: 0.5912 REMARK 3 L33: 3.9433 L12: -1.5281 REMARK 3 L13: -4.5912 L23: 1.4996 REMARK 3 S TENSOR REMARK 3 S11: 0.4337 S12: -0.6217 S13: 0.8265 REMARK 3 S21: 0.5320 S22: -0.1059 S23: -0.2458 REMARK 3 S31: 0.0754 S32: 0.2677 S33: -0.3495 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 16 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.5613 0.7189 -0.1225 REMARK 3 T TENSOR REMARK 3 T11: 0.9294 T22: 0.7753 REMARK 3 T33: 0.7220 T12: -0.0650 REMARK 3 T13: 0.0948 T23: 0.0413 REMARK 3 L TENSOR REMARK 3 L11: 8.4421 L22: 8.0988 REMARK 3 L33: 3.0336 L12: -4.5124 REMARK 3 L13: 3.7033 L23: -1.1194 REMARK 3 S TENSOR REMARK 3 S11: 0.3081 S12: 1.1524 S13: 0.4618 REMARK 3 S21: -0.6245 S22: -0.1638 S23: -0.2985 REMARK 3 S31: -0.7332 S32: 0.7368 S33: 0.0943 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 25 THROUGH 34 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.4932 -6.7175 1.3656 REMARK 3 T TENSOR REMARK 3 T11: 0.6130 T22: 0.5781 REMARK 3 T33: 0.6760 T12: 0.0519 REMARK 3 T13: 0.0344 T23: 0.0614 REMARK 3 L TENSOR REMARK 3 L11: 9.7095 L22: 4.7688 REMARK 3 L33: 4.7367 L12: 4.3819 REMARK 3 L13: 3.6134 L23: 4.0081 REMARK 3 S TENSOR REMARK 3 S11: -0.1261 S12: 0.2514 S13: 0.2751 REMARK 3 S21: 0.1625 S22: -0.0441 S23: 0.4421 REMARK 3 S31: 0.4080 S32: -0.2312 S33: 0.1985 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 35 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.3165 -24.6407 -5.3962 REMARK 3 T TENSOR REMARK 3 T11: 0.9581 T22: 0.8328 REMARK 3 T33: 0.9395 T12: -0.0468 REMARK 3 T13: -0.0635 T23: -0.0277 REMARK 3 L TENSOR REMARK 3 L11: 7.3460 L22: 8.0808 REMARK 3 L33: 0.8114 L12: 6.1179 REMARK 3 L13: 1.2248 L23: 0.1851 REMARK 3 S TENSOR REMARK 3 S11: -0.3985 S12: 0.2164 S13: -0.5238 REMARK 3 S21: -0.3209 S22: 0.1344 S23: -0.5703 REMARK 3 S31: 0.1239 S32: -0.0494 S33: 0.2699 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 21LD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1300067420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6189 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 REMARK 200 RESOLUTION RANGE LOW (A) : 54.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 1.96800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE 0.1 M SODIUM REMARK 280 CACODYLATE TRIHYDRATE PH 6.2 34% MPD 10MM TCEP HYDROCHLORIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.29050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.94000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.94000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.64525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.94000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.94000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.93575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.94000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.94000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.64525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.94000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.94000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.93575 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 41.29050 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 A D 45 O3' - P - OP2 ANGL. DEV. = -18.1 DEGREES REMARK 500 A D 45 O3' - P - OP1 ANGL. DEV. = -24.5 DEGREES REMARK 500 A D 45 OP1 - P - OP2 ANGL. DEV. = 9.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 21LD B 1 14 PDB 21LD 21LD 1 14 DBREF 21LD C 1 24 PDB 21LD 21LD 1 24 DBREF 21LD D 25 48 PDB 21LD 21LD 25 48 SEQRES 1 B 14 C C A C U G C G A G U U U SEQRES 2 B 14 C SEQRES 1 C 24 G G A A G C U C U G A C C SEQRES 2 C 24 G A C C C C C A G C C SEQRES 1 D 24 G C U G G G A C A A C U A SEQRES 2 D 24 G A C A U A C A G U G HET GUN D 101 16 HETNAM GUN GUANINE FORMUL 4 GUN C5 H5 N5 O FORMUL 5 HOH *2(H2 O) CRYST1 71.880 71.880 82.581 90.00 90.00 90.00 P 41 21 2 8 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 0.013912 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013912 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012109 0.00000 CONECT 1991 1992 2001 2002 CONECT 1992 1991 1993 2003 CONECT 1993 1992 1994 CONECT 1994 1993 1995 2001 CONECT 1995 1994 1996 1997 CONECT 1996 1995 CONECT 1997 1995 1998 2004 CONECT 1998 1997 1999 2000 CONECT 1999 1998 2005 2006 CONECT 2000 1998 2001 CONECT 2001 1991 1994 2000 CONECT 2002 1991 CONECT 2003 1992 CONECT 2004 1997 CONECT 2005 1999 CONECT 2006 1999 MASTER 301 0 1 0 0 0 0 6 1322 3 16 6 END