PDB Short entry for 3DW5 HEADER RNA 21-JUL-08 3DW5 TITLE CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23S RRNA, TITLE 2 U2656-OCH3 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 5 30-AUG-23 3DW5 1 LINK REVDAT 4 25-OCT-17 3DW5 1 REMARK REVDAT 3 11-AUG-10 3DW5 1 JRNL REVDAT 2 19-JAN-10 3DW5 1 REMARK REVDAT 1 24-MAR-09 3DW5 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. 0.96 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) : 0.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 39656 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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 27.5690 - 2.3130 1.00 2729 145 0.1490 0.1680 REMARK 3 2 2.3130 - 1.8360 1.00 2682 155 0.1590 0.1680 REMARK 3 3 1.8360 - 1.6040 1.00 2708 155 0.1310 0.1540 REMARK 3 4 1.6040 - 1.4570 1.00 2710 137 0.1410 0.1460 REMARK 3 5 1.4570 - 1.3530 1.00 2672 144 0.1470 0.1700 REMARK 3 6 1.3530 - 1.2730 1.00 2702 140 0.1420 0.1430 REMARK 3 7 1.2730 - 1.2090 1.00 2725 139 0.1400 0.1390 REMARK 3 8 1.2090 - 1.1570 1.00 2673 146 0.1400 0.1470 REMARK 3 9 1.1570 - 1.1120 1.00 2710 137 0.1390 0.1650 REMARK 3 10 1.1120 - 1.0740 1.00 2652 151 0.1410 0.1630 REMARK 3 11 1.0740 - 1.0400 1.00 2729 131 0.1510 0.1580 REMARK 3 12 1.0400 - 1.0110 1.00 2682 143 0.1600 0.1810 REMARK 3 13 1.0110 - 0.9840 1.00 2664 136 0.1760 0.1900 REMARK 3 14 0.9840 - 0.9600 0.97 2623 136 0.2000 0.2410 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 : 0.44 REMARK 3 B_SOL : 39.75 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.25000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : 0.50000 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 : 0.004 704 REMARK 3 ANGLE : 1.141 1099 REMARK 3 CHIRALITY : 0.054 142 REMARK 3 PLANARITY : 0.006 29 REMARK 3 DIHEDRAL : 31.317 309 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 3DW5 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_1000048563. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-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 : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.85 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39656 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.960 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.63400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1Q9A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.25 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 38.08000 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 57.12000 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 19.04000 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q9A RELATED DB: PDB REMARK 900 RELATED ID: 3DVZ RELATED DB: PDB REMARK 900 RELATED ID: 3DW4 RELATED DB: PDB REMARK 900 RELATED ID: 3DW6 RELATED DB: PDB REMARK 900 RELATED ID: 3DW7 RELATED DB: PDB REMARK 900 RELATED ID: 483D RELATED DB: PDB DBREF 3DW5 A 2647 2673 PDB 3DW5 3DW5 2647 2673 SEQRES 1 A 27 U G C U C C U A G OMU 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 3DW5 OMU A 2656 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE HET OMU A2656 21 HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE FORMUL 1 OMU C10 H15 N2 O9 P FORMUL 2 HOH *146(H2 O) LINK O3' G A2655 P OMU A2656 1555 1555 1.60 LINK O3' OMU A2656 P A A2657 1555 1555 1.60 CRYST1 29.560 29.560 76.160 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 0.033829 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013130 0.00000