HEADER DNA 15-JUL-15 5CKI TITLE CRYSTAL STRUCTURE OF 9DB1* DEOXYRIBOZYME (COBALT HEXAMMINE SOAKED TITLE 2 CRYSTALS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(P*GP*CP*AP*CP*UP*AP*GP*AP*UP*CP*GP*GP*AP*UP*G)- COMPND 3 3'); COMPND 4 CHAIN: D; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (44-MER); COMPND 8 CHAIN: Y; COMPND 9 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 KEYWDS DEOXYRIBOZYME, RNA-LIGASE, CATALYTIC DNA, DNA EXPDTA X-RAY DIFFRACTION AUTHOR A.PONCE-SALVATIERRA,C.HOEBARTNER,V.PENA REVDAT 2 20-JAN-16 5CKI 1 JRNL REVDAT 1 13-JAN-16 5CKI 0 JRNL AUTH A.PONCE-SALVATIERRA,K.WAWRZYNIAK-TUREK,U.STEUERWALD, JRNL AUTH 2 C.HOBARTNER,V.PENA JRNL TITL CRYSTAL STRUCTURE OF A DNA CATALYST. JRNL REF NATURE V. 529 231 2016 JRNL REFN ESSN 1476-4687 JRNL PMID 26735012 JRNL DOI 10.1038/NATURE16471 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10PRE_2086 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 4053 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.256 REMARK 3 FREE R VALUE : 0.311 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 356 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 45.9360 - 4.3040 1.00 2273 117 0.2168 0.2633 REMARK 3 2 4.3040 - 3.4170 1.00 2292 120 0.3427 0.4114 REMARK 3 3 3.4170 - 2.9853 0.98 2239 119 0.3878 0.4232 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 1380 REMARK 3 ANGLE : 0.599 2134 REMARK 3 CHIRALITY : 0.029 251 REMARK 3 PLANARITY : 0.004 59 REMARK 3 DIHEDRAL : 28.985 614 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'D' OR CHAIN 'Y' REMARK 3 ORIGIN FOR THE GROUP (A): 22.9316 4.7277 22.6955 REMARK 3 T TENSOR REMARK 3 T11: 1.0539 T22: 1.2921 REMARK 3 T33: 1.1304 T12: 0.1146 REMARK 3 T13: -0.0926 T23: -0.1458 REMARK 3 L TENSOR REMARK 3 L11: 2.6182 L22: 4.2460 REMARK 3 L33: 2.8653 L12: -0.3343 REMARK 3 L13: -0.7690 L23: -0.7477 REMARK 3 S TENSOR REMARK 3 S11: -0.0556 S12: -0.1105 S13: -0.1967 REMARK 3 S21: -0.5832 S22: 0.2188 S23: 0.8572 REMARK 3 S31: 0.2211 S32: -0.2552 S33: -0.1028 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 5CKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211357. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.604 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4060 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 45.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 24.00 REMARK 200 R MERGE FOR SHELL (I) : 3.99000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SPERMINE, MAGNESIUM CHLORIDE, REMARK 280 SODIUM CHLORIDE, SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 27.90700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.42250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.42250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.86050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.42250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.42250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.95350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.42250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.42250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.86050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.42250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.42250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.95350 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 27.90700 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, Y 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 DA Y 14A 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 CO D 101 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A D -1 N7 REMARK 620 2 A D -1 N6 76.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO Y 102 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG Y 8 N7 REMARK 620 2 DG Y 25 OP2 72.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG Y 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT Y 14 OP1 REMARK 620 2 DA Y 15 OP1 104.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO D 102 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G D -6 N7 REMARK 620 2 G D -6 C5 30.4 REMARK 620 3 G D -6 O6 80.3 52.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO Y 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO Y 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG Y 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG Y 104 DBREF 5CKI D -6 9 PDB 5CKI 5CKI -6 9 DBREF 5CKI Y 1 44 PDB 5CKI 5CKI 1 44 SEQRES 1 D 15 G C A C U A G A U C G G A SEQRES 2 D 15 U G SEQRES 1 Y 45 DA DT DC DC DG DA DT DG DG DA DT DC DA SEQRES 2 Y 45 DT DA DA DC DG DG DT DC DG DG DA DG DG SEQRES 3 Y 45 DG DG DT DT DT DG DC DC DG DT DT DT DA SEQRES 4 Y 45 DA DG DT DG DC DC HET CO D 101 1 HET CO D 102 1 HET CO Y 101 1 HET CO Y 102 1 HET MG Y 103 1 HET MG Y 104 1 HETNAM CO COBALT (II) ION HETNAM MG MAGNESIUM ION FORMUL 3 CO 4(CO 2+) FORMUL 7 MG 2(MG 2+) LINK N7 A D -1 CO CO D 101 1555 1555 2.20 LINK N6 A D -1 CO CO D 101 1555 1555 2.75 LINK N7 DG Y 8 CO CO Y 102 1555 1555 2.73 LINK OP1 DT Y 14 MG MG Y 104 1555 1555 2.14 LINK OP1 DA Y 15 MG MG Y 104 1555 1555 2.01 LINK OP2 DA Y 15 MG MG Y 103 1555 1555 2.04 LINK OP2 DG Y 25 CO CO Y 102 1555 1555 2.23 LINK N7 DA Y 39 CO CO Y 101 1555 1555 2.16 LINK N7 G D -6 CO CO D 102 1555 3545 1.91 LINK C5 G D -6 CO CO D 102 1555 3545 2.64 LINK O6 G D -6 CO CO D 102 1555 3545 2.76 SITE 1 AC1 2 A D -1 G D 1 SITE 1 AC2 3 G D -6 U D 8 G D 9 SITE 1 AC3 1 DA Y 39 SITE 1 AC4 2 DG Y 8 DG Y 25 SITE 1 AC5 1 DA Y 15 SITE 1 AC6 2 DT Y 14 DA Y 15 CRYST1 80.845 80.845 55.814 90.00 90.00 90.00 P 43 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 0.012369 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012369 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017917 0.00000