HEADER RNA 14-MAR-12 4E58 TITLE CRYSTAL STRUCTURE OF GCC(LCG)CCGC DUPLEX CONTAINING LNA RESIDUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DUPLEX CONTAINING CCG REPEATS; COMPND 3 CHAIN: C, E, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: SIMILAR SEQUENCES OCCUR IN MRNA IN HUMANS KEYWDS CCG REPEATS, 5' SLIPPERY DUPLEXES, X-LINKED MENTAL RETARDATION, KEYWDS 2 HUNTINGTON'S DISEASE, MYOTONIC DYSTROPHY TYPE 1, LNA GUANOSINE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.KILISZEK,R.KIERZEK,W.J.KRZYZOSIAK,R.RYPNIEWSKI REVDAT 3 13-SEP-23 4E58 1 REMARK LINK REVDAT 2 15-NOV-17 4E58 1 SOURCE REMARK REVDAT 1 12-DEC-12 4E58 0 JRNL AUTH A.KILISZEK,R.KIERZEK,W.J.KRZYZOSIAK,W.RYPNIEWSKI JRNL TITL CRYSTALLOGRAPHIC CHARACTERIZATION OF CCG REPEATS. JRNL REF NUCLEIC ACIDS RES. V. 40 8155 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22718980 JRNL DOI 10.1093/NAR/GKS557 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 5717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 100.00 REMARK 3 FREE R VALUE TEST SET COUNT : 562 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 2.1486 - 1.9520 0.97 179 129 0.3766 0.4417 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.49 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 36.22 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.35250 REMARK 3 B22 (A**2) : 6.35250 REMARK 3 B33 (A**2) : -12.70500 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 : 0.010 549 REMARK 3 ANGLE : 1.230 856 REMARK 3 CHIRALITY : 0.066 110 REMARK 3 PLANARITY : 0.012 23 REMARK 3 DIHEDRAL : 16.246 252 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 4E58 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071184. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9148 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 28.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 15.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.67300 REMARK 200 FOR SHELL : 2.175 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3GLP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, MGCL2 AND LI2SO4, PH 5.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 40.82800 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 61.24200 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 20.41400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 40.82800 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 20.41400 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 61.24200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 20.41400 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH D 203 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 C E 8 C4' O4' C3' O3' C2' O2' C1' REMARK 470 C E 8 N1 C2 O2 N3 C4 N4 C5 REMARK 470 C E 8 C6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E59 RELATED DB: PDB DBREF 4E58 C 1 8 PDB 4E58 4E58 1 8 DBREF 4E58 E 1 8 PDB 4E58 4E58 1 8 DBREF 4E58 D 1 8 PDB 4E58 4E58 1 8 SEQRES 1 C 8 G C C LCG C C G C SEQRES 1 E 8 G C C LCG C C G C SEQRES 1 D 8 G C C LCG C C G C MODRES 4E58 LCG C 4 DG MODRES 4E58 LCG E 4 DG MODRES 4E58 LCG D 4 DG HET LCG C 4 24 HET LCG E 4 24 HET LCG D 4 24 HET SO4 C 101 5 HET SO4 D 101 5 HETNAM LCG [(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5- HETNAM 2 LCG DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 LCG PHOSPHATE HETNAM SO4 SULFATE ION FORMUL 1 LCG 3(C11 H14 N5 O8 P) FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *14(H2 O) LINK O3' C C 3 P LCG C 4 1555 1555 1.60 LINK O3' LCG C 4 P C C 5 1555 1555 1.59 LINK O3' C E 3 P LCG E 4 1555 1555 1.61 LINK O3' LCG E 4 P C E 5 1555 1555 1.60 LINK O3' C D 3 P LCG D 4 1555 1555 1.60 LINK O3' LCG D 4 P C D 5 1555 1555 1.61 SITE 1 AC1 3 C C 2 C C 3 HOH C 202 SITE 1 AC2 4 G C 7 C C 8 LCG D 4 C D 5 CRYST1 42.016 42.016 81.656 90.00 90.00 90.00 P 43 2 2 24 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 0.023800 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012246 0.00000