HEADER RNA 18-AUG-16 5LR3 TITLE RNA DUPLEX HAS CENTRAL CONSECUTIVE GA PAIRS FLANKED BY G-U BASEPAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*AP*UP*GP*GP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS N6-METHYLADENINE, RNA FOLDING, WATSON-CRICK BASEPAIRS, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.HUANG,D.M.J.LILLEY REVDAT 3 13-SEP-17 5LR3 1 JRNL REVDAT 2 28-JUN-17 5LR3 1 JRNL REVDAT 1 21-JUN-17 5LR3 0 JRNL AUTH L.HUANG,S.ASHRAF,J.WANG,D.M.LILLEY JRNL TITL CONTROL OF BOX C/D SNORNP ASSEMBLY BY N(6)-METHYLATION OF JRNL TITL 2 ADENINE. JRNL REF EMBO REP. V. 18 1631 2017 JRNL REFN ESSN 1469-3178 JRNL PMID 28623187 JRNL DOI 10.15252/EMBR.201743967 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2481: ???) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 8701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 739 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 29.1724 - 2.8209 0.98 2951 132 0.1919 0.2043 REMARK 3 2 2.8209 - 2.2393 0.99 2928 154 0.2976 0.3394 REMARK 3 3 2.2393 - 1.9563 0.99 2930 171 0.3055 0.3008 REMARK 3 4 1.9563 - 1.7774 0.99 2963 153 0.3560 0.3675 REMARK 3 5 1.7774 - 1.6501 0.96 2858 129 0.4054 0.3714 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.010 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 : 0.001 486 REMARK 3 ANGLE : 2.499 760 REMARK 3 CHIRALITY : 0.018 96 REMARK 3 PLANARITY : 0.003 20 REMARK 3 DIHEDRAL : 9.510 216 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:4) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4186 -18.2399 15.0204 REMARK 3 T TENSOR REMARK 3 T11: 0.9995 T22: 0.2801 REMARK 3 T33: 0.3946 T12: -0.0017 REMARK 3 T13: 0.0152 T23: 0.0443 REMARK 3 L TENSOR REMARK 3 L11: 2.0382 L22: 0.4342 REMARK 3 L33: 1.6172 L12: 0.1630 REMARK 3 L13: 0.0223 L23: 0.8277 REMARK 3 S TENSOR REMARK 3 S11: 0.7857 S12: 0.0847 S13: -0.0838 REMARK 3 S21: -1.0240 S22: -0.2580 S23: -0.1488 REMARK 3 S31: 0.2197 S32: -0.1246 S33: -0.4835 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 5:10) REMARK 3 ORIGIN FOR THE GROUP (A): -3.1101 -14.5796 0.5231 REMARK 3 T TENSOR REMARK 3 T11: 0.5471 T22: 0.3102 REMARK 3 T33: 0.2989 T12: -0.0299 REMARK 3 T13: -0.0014 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 2.7298 L22: 2.6603 REMARK 3 L33: 2.8577 L12: -0.1443 REMARK 3 L13: 0.2258 L23: -0.4158 REMARK 3 S TENSOR REMARK 3 S11: 0.2171 S12: 0.1307 S13: -0.4820 REMARK 3 S21: 0.0769 S22: -0.0974 S23: 0.4692 REMARK 3 S31: 1.4485 S32: 0.1220 S33: -0.1938 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN B AND RESID 1:5) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5467 -9.2098 1.6537 REMARK 3 T TENSOR REMARK 3 T11: 0.4902 T22: 0.3216 REMARK 3 T33: 0.3464 T12: 0.0679 REMARK 3 T13: -0.0285 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 0.7854 L22: 2.6164 REMARK 3 L33: 3.0169 L12: 0.2001 REMARK 3 L13: 1.4495 L23: -0.4496 REMARK 3 S TENSOR REMARK 3 S11: 0.0345 S12: -0.0755 S13: 0.0296 REMARK 3 S21: 0.6547 S22: -0.0934 S23: 0.0366 REMARK 3 S31: 1.1169 S32: 1.0789 S33: 0.0393 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 6:10) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3140 -23.4444 14.8468 REMARK 3 T TENSOR REMARK 3 T11: 1.2218 T22: 0.3525 REMARK 3 T33: 0.4390 T12: -0.0665 REMARK 3 T13: -0.1096 T23: 0.0840 REMARK 3 L TENSOR REMARK 3 L11: 0.3622 L22: 0.0508 REMARK 3 L33: 0.6843 L12: -0.0513 REMARK 3 L13: -0.4922 L23: 0.0428 REMARK 3 S TENSOR REMARK 3 S11: 0.3426 S12: 0.1189 S13: 0.1528 REMARK 3 S21: -0.2958 S22: -0.2566 S23: 0.0528 REMARK 3 S31: -0.2109 S32: -0.0339 S33: -0.2438 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 5LR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200001229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8761 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 29.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 1.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.015 M MAGNESIUM ACETATE, 0.05 M REMARK 280 SODIUM CACODYLATE PH 6.0, 1.7 M AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 60.45500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 16.65000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 16.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 90.68250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 16.65000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 16.65000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.22750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 16.65000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 16.65000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 90.68250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 16.65000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 16.65000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.22750 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 60.45500 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: 2570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G B 1 and CBV B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide CBV B 2 and C B 3 DBREF 5LR3 A 1 10 PDB 5LR3 5LR3 1 10 DBREF 5LR3 B 1 10 PDB 5LR3 5LR3 1 10 SEQRES 1 A 10 G CBV C G G A U G G C SEQRES 1 B 10 G CBV C G G A U G G C HET CBV A 2 22 HET CBV B 2 22 HET SO4 B 101 5 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM SO4 SULFATE ION FORMUL 1 CBV 2(C9 H13 BR N3 O8 P) FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *33(H2 O) LINK O3' G A 1 P CBV A 2 1555 1555 1.61 LINK O3' CBV A 2 P C A 3 1555 1555 1.61 LINK O3' G B 1 P CBV B 2 1555 1555 1.61 LINK O3' CBV B 2 P C B 3 1555 1555 1.61 SITE 1 AC1 4 G B 1 CBV B 2 HOH B 201 HOH B 207 SITE 1 AC2 10 G A 1 G A 9 C A 10 C B 3 SITE 2 AC2 10 C B 10 SO4 B 101 HOH B 201 HOH B 207 SITE 3 AC2 10 HOH B 212 HOH B 214 SITE 1 AC3 10 G A 8 G A 9 C A 10 G B 1 SITE 2 AC3 10 G B 4 SO4 B 101 HOH B 207 HOH B 209 SITE 3 AC3 10 HOH B 212 HOH B 214 CRYST1 33.300 33.300 120.910 90.00 90.00 90.00 P 43 21 2 16 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 0.030030 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030030 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008271 0.00000