HEADER RNA 21-JUL-08 3DW6 TITLE CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA, TITLE 2 U2650-SECH3 MODIFIED COMPND MOL_ID: 1; COMPND 2 MOLECULE: SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RNA, SARCIN RICIN LOOP EXPDTA X-RAY DIFFRACTION AUTHOR V.OLIERIC,U.RIEDER,K.LANG,A.SERGANOV,C.SCHULZE-BRIESE,R.MICURA, AUTHOR 2 P.DUMAS,E.ENNIFAR REVDAT 4 21-FEB-24 3DW6 1 REMARK LINK REVDAT 3 13-JUL-11 3DW6 1 VERSN REVDAT 2 11-AUG-10 3DW6 1 JRNL REVDAT 1 24-MAR-09 3DW6 0 JRNL AUTH V.OLIERIC,U.RIEDER,K.LANG,A.SERGANOV,C.SCHULZE-BRIESE, JRNL AUTH 2 R.MICURA,P.DUMAS,E.ENNIFAR JRNL TITL A FAST SELENIUM DERIVATIZATION STRATEGY FOR CRYSTALLIZATION JRNL TITL 2 AND PHASING OF RNA STRUCTURES. JRNL REF RNA V. 15 707 2009 JRNL REFN ISSN 1355-8382 JRNL PMID 19228585 JRNL DOI 10.1261/RNA.1499309 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 64959 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3256 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 20.1930 - 2.8420 0.97 2829 132 0.1190 0.1170 REMARK 3 2 2.8420 - 2.2560 0.99 2858 165 0.1500 0.1900 REMARK 3 3 2.2560 - 1.9710 1.00 2889 149 0.1370 0.1530 REMARK 3 4 1.9710 - 1.7910 1.00 2891 172 0.1220 0.1500 REMARK 3 5 1.7910 - 1.6630 1.00 2854 171 0.1110 0.1240 REMARK 3 6 1.6630 - 1.5650 1.00 2900 135 0.1110 0.1420 REMARK 3 7 1.5650 - 1.4870 1.00 2897 150 0.1260 0.1330 REMARK 3 8 1.4870 - 1.4220 1.00 2901 178 0.1180 0.1250 REMARK 3 9 1.4220 - 1.3670 1.00 2903 141 0.1210 0.1270 REMARK 3 10 1.3670 - 1.3200 1.00 2896 172 0.1180 0.1700 REMARK 3 11 1.3200 - 1.2790 1.00 2864 168 0.1230 0.1530 REMARK 3 12 1.2790 - 1.2420 1.00 2923 145 0.1140 0.1230 REMARK 3 13 1.2420 - 1.2090 1.00 2918 137 0.1150 0.1280 REMARK 3 14 1.2090 - 1.1800 1.00 2872 161 0.1230 0.1380 REMARK 3 15 1.1800 - 1.1530 1.00 2939 182 0.1230 0.1520 REMARK 3 16 1.1530 - 1.1290 1.00 2821 156 0.1380 0.1510 REMARK 3 17 1.1290 - 1.1060 0.99 2857 178 0.1470 0.1820 REMARK 3 18 1.1060 - 1.0850 0.95 2775 118 0.1580 0.1770 REMARK 3 19 1.0850 - 1.0660 0.85 2471 122 0.1790 0.1970 REMARK 3 20 1.0660 - 1.0480 0.77 2288 84 0.1980 0.1960 REMARK 3 21 1.0480 - 1.0310 0.66 1961 78 0.2200 0.2040 REMARK 3 22 1.0310 - 1.0150 0.60 1703 93 0.2500 0.2790 REMARK 3 23 1.0150 - 1.0000 0.51 1493 69 0.2990 0.3190 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 : 0.46 REMARK 3 B_SOL : 60.32 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.19100 REMARK 3 B22 (A**2) : -2.19100 REMARK 3 B33 (A**2) : 0.95700 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 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 : 0.005 666 REMARK 3 ANGLE : 1.268 1044 REMARK 3 CHIRALITY : 0.055 131 REMARK 3 PLANARITY : 0.012 27 REMARK 3 DIHEDRAL : 26.164 293 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 3DW6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.97916 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64959 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 16.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.41700 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M (NH4)2SO4, 50 MM K-MOPS PH 7.0, REMARK 280 10 MM MGCL2, 10 MM MNCL2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 38.26500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.39750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.13250 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 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q9A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E.COLI 23S RRNA REMARK 900 AT 1.04 RESOLUTION REMARK 900 RELATED ID: 3DVZ RELATED DB: PDB REMARK 900 RELATED ID: 3DW4 RELATED DB: PDB REMARK 900 RELATED ID: 3DW5 RELATED DB: PDB REMARK 900 RELATED ID: 3DW7 RELATED DB: PDB REMARK 900 RELATED ID: 483D RELATED DB: PDB DBREF 3DW6 A 2647 2673 PDB 3DW6 3DW6 2647 2673 SEQRES 1 A 27 U G C UMS C C U A G U A C G SEQRES 2 A 27 A G A G G A C C G G A G U SEQRES 3 A 27 G MODRES 3DW6 UMS A 2650 DU HET UMS A2650 21 HET GOL A 1 14 HETNAM UMS 2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 UMS C10 H15 N2 O8 P SE FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *184(H2 O) LINK O3' C A2649 P UMS A2650 1555 1555 1.59 LINK O3' UMS A2650 P C A2651 1555 1555 1.60 SITE 1 AC1 10 U A2647 U A2653 A A2654 U A2656 SITE 2 AC1 10 A A2660 C A2666 HOH A2719 HOH A2757 SITE 3 AC1 10 HOH A2802 HOH A2841 CRYST1 29.600 29.600 76.530 90.00 90.00 90.00 P 43 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 0.033784 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033784 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013067 0.00000