HEADER RNA 02-JUL-18 6GYV TITLE LARIAT-CAPPING RIBOZYME (CIRCULAR PERMUTATION FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LARIAT-CAPPING RIBOZYME; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DIDYMIUM IRIDIS; SOURCE 4 ORGANISM_TAXID: 5793 KEYWDS LARIAT CAPPING RIBOZYME, RNA EXPDTA X-RAY DIFFRACTION AUTHOR B.MASQUIDA,M.MEYER,H.NIELSEN,V.OLIERIC,P.ROBLIN,S.D.JOHANSEN, AUTHOR 2 E.WESTHOF REVDAT 3 31-JAN-24 6GYV 1 REMARK REVDAT 2 14-DEC-22 6GYV 1 EXPDTA LINK REVDAT 1 22-AUG-18 6GYV 0 SPRSDE 22-AUG-18 6GYV 4P95 JRNL AUTH M.MEYER,H.NIELSEN,V.OLIERIC,P.ROBLIN,S.D.JOHANSEN,E.WESTHOF, JRNL AUTH 2 B.MASQUIDA JRNL TITL SPECIATION OF A GROUP I INTRON INTO A LARIAT CAPPING JRNL TITL 2 RIBOZYME. JRNL REF PROC. NATL. ACAD. SCI. V. 111 7659 2014 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 24821772 JRNL DOI 10.1073/PNAS.1322248111 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11RC1_2513 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.592 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 34663 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.678 REMARK 3 FREE R VALUE TEST SET COUNT : 1968 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 47.8332 - 6.0217 0.99 2394 135 0.1716 0.1924 REMARK 3 2 6.0217 - 4.7810 0.98 2401 134 0.1549 0.1905 REMARK 3 3 4.7810 - 4.1771 0.98 2381 142 0.1566 0.1854 REMARK 3 4 4.1771 - 3.7953 0.97 2399 116 0.1558 0.2019 REMARK 3 5 3.7953 - 3.5234 0.97 2308 163 0.1710 0.2019 REMARK 3 6 3.5234 - 3.3157 0.97 2337 158 0.1957 0.2382 REMARK 3 7 3.3157 - 3.1497 0.97 2355 126 0.2011 0.2842 REMARK 3 8 3.1497 - 3.0126 0.96 2355 110 0.2237 0.2934 REMARK 3 9 3.0126 - 2.8967 0.96 2315 141 0.2801 0.3630 REMARK 3 10 2.8967 - 2.7967 0.96 2315 147 0.3005 0.3130 REMARK 3 11 2.7967 - 2.7093 0.96 2292 150 0.2905 0.4317 REMARK 3 12 2.7093 - 2.6318 0.95 2277 173 0.2988 0.3421 REMARK 3 13 2.6318 - 2.5626 0.95 2277 145 0.3076 0.3676 REMARK 3 14 2.5626 - 2.5000 0.94 2289 128 0.3111 0.3508 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.399 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.30 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 4605 REMARK 3 ANGLE : 0.521 7182 REMARK 3 CHIRALITY : 0.023 959 REMARK 3 PLANARITY : 0.002 192 REMARK 3 DIHEDRAL : 13.582 2309 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6GYV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200009556. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.6 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34663 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 47.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: 4P9R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 SODIUM CHLORIDE, 0.1 M BIS-TRIS PH REMARK 280 6.5, 25% W/V PEG 3,350 OR (II) 0.2 SODIUM CHLORIDE, 0.1 M HEPES REMARK 280 PH 7.5, 25% W/V PEG 3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 28.81500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.26500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.85500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.26500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.81500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.85500 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: 690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 U A 155A REMARK 465 U A 155B 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 OP2 A A 95 O2' G A 131 2.15 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 U A 85 C2 - N1 - C1' ANGL. DEV. = 8.2 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 133 OP1 REMARK 620 2 HOH A 329 O 94.8 REMARK 620 3 HOH A 363 O 172.8 89.8 REMARK 620 4 HOH A 366 O 84.4 90.1 90.0 REMARK 620 5 HOH A 370 O 85.2 179.9 90.2 89.9 REMARK 620 6 HOH A 373 O 95.6 90.1 89.9 179.8 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 306 O REMARK 620 2 HOH A 315 O 179.7 REMARK 620 3 HOH A 330 O 89.9 89.8 REMARK 620 4 HOH A 332 O 90.0 90.2 89.9 REMARK 620 5 HOH A 356 O 90.2 90.1 179.9 90.0 REMARK 620 6 HOH A 399 O 89.9 89.9 90.3 179.8 89.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P8Z RELATED DB: PDB REMARK 900 SAME RIBOZYME WT REMARK 900 RELATED ID: 4P9R RELATED DB: PDB REMARK 900 LC RIBOZYME IRIDIUM HEXAMMINE DERIVATIVE DBREF 6GYV A 1 190 PDB 6GYV 6GYV 1 190 SEQRES 1 A 192 C A U C C G G U A U C C C SEQRES 2 A 192 A A G A C A A U C U U C G SEQRES 3 A 192 G G U U G G G U U G G G A SEQRES 4 A 192 A G U A U C A U G G C U A SEQRES 5 A 192 A U C A C C A U G A U G C SEQRES 6 A 192 A A U C G G G U U G A A C SEQRES 7 A 192 A C U U A A U U G G G U U SEQRES 8 A 192 A A A A C G G U G G G G G SEQRES 9 A 192 A C G A U C C C G U A A C SEQRES 10 A 192 A U C C G U C C U A A C G SEQRES 11 A 192 G C G A C A G A C U G C A SEQRES 12 A 192 C G G C C C U G C C U C U SEQRES 13 A 192 U A G G U G U G U C C A A SEQRES 14 A 192 U G A A C A G U C G U U C SEQRES 15 A 192 C G A A A G G A A G HET MES A 201 12 HET MG A 202 1 HET MG A 203 1 HET NA A 204 1 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 2 MES C6 H13 N O4 S FORMUL 3 MG 2(MG 2+) FORMUL 5 NA NA 1+ FORMUL 6 HOH *99(H2 O) LINK OP1 G A 133 MG MG A 202 1555 1555 2.08 LINK O1 MES A 201 NA NA A 204 1555 1555 2.80 LINK MG MG A 202 O HOH A 329 1555 1555 2.18 LINK MG MG A 202 O HOH A 363 1555 1555 2.18 LINK MG MG A 202 O HOH A 366 1555 1555 2.18 LINK MG MG A 202 O HOH A 370 1555 1555 2.18 LINK MG MG A 202 O HOH A 373 1555 1555 2.18 LINK MG MG A 203 O HOH A 306 1555 1555 2.19 LINK MG MG A 203 O HOH A 315 1555 1555 2.19 LINK MG MG A 203 O HOH A 330 1555 1555 2.18 LINK MG MG A 203 O HOH A 332 1555 1555 2.18 LINK MG MG A 203 O HOH A 356 1555 1555 2.18 LINK MG MG A 203 O HOH A 399 1555 1555 2.18 SITE 1 AC1 6 A A 167 U A 168 C A 172 A A 173 SITE 2 AC1 6 NA A 204 HOH A 305 SITE 1 AC2 6 G A 133 HOH A 329 HOH A 363 HOH A 366 SITE 2 AC2 6 HOH A 370 HOH A 373 SITE 1 AC3 6 HOH A 306 HOH A 315 HOH A 330 HOH A 332 SITE 2 AC3 6 HOH A 356 HOH A 399 SITE 1 AC4 5 C A 1 U A 3 C A 142 A A 167 SITE 2 AC4 5 MES A 201 CRYST1 57.630 85.710 108.530 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 0.017352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009214 0.00000