HEADER RNA 25-MAY-96 310D TITLE CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.3 A TITLE 2 RESOLUTION. HYDRATION PATTERN OF 2'-O-METHYLATED RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630 KEYWDS A-RNA, DOUBLE HELIX, MODIFIED, RNA EXPDTA X-RAY DIFFRACTION AUTHOR D.A.ADAMIAK,J.MILECKI,R.W.ADAMIAK,Z.DAUTER,W.R.RYPNIEWSKI REVDAT 4 24-JUN-20 310D 1 SOURCE REMARK DBREF LINK REVDAT 3 24-FEB-09 310D 1 VERSN REVDAT 2 01-APR-03 310D 1 JRNL REVDAT 1 24-JUN-97 310D 0 JRNL AUTH D.A.ADAMIAK,J.MILECKI,M.POPENDA,R.W.ADAMIAK,Z.DAUTER, JRNL AUTH 2 W.R.RYPNIEWSKI JRNL TITL CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2, AN RNA DUPLEX AT 1.30 JRNL TITL 2 A RESOLUTION. HYDRATION PATTERN OF 2'-O-METHYLATED RNA. JRNL REF NUCLEIC ACIDS RES. V. 25 4599 1997 JRNL REFN ISSN 0305-1048 JRNL PMID 9358171 JRNL DOI 10.1093/NAR/25.22.4599 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.POPENDA,E.BIALA,J.MILECKI,R.W.ADAMIAK REMARK 1 TITL LOW SALT NMR STUDY OF R(CGCGCG) AND 2'-O-ME(CGCGCG) REVEALS REMARK 1 TITL 2 STRUCTURE OF RNA DUPLEXES CONTAINING CONSECUTIVE CG BASE REMARK 1 TITL 3 PAIRS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-96 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.172 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8165 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.163 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6979 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 264 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 154.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 295.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2778 REMARK 3 NUMBER OF RESTRAINTS : 3275 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.025 REMARK 3 ANGLE DISTANCES (A) : 0.000 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.098 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.032 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.085 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS, KRETSINGER, J.MOL.BIOL. 91(1973)201 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : CCP4 DICTIONARY REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 310D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000178778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-95 REMARK 200 TEMPERATURE (KELVIN) : 277.00 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : TRIANGULAR GE CRYSTAL REMARK 200 OPTICS : SEGMENTED MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8165 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: ARN035 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.63333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 107.26667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 80.45000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 134.08333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.81667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.63333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 107.26667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 134.08333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 80.45000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 26.81667 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: DIMERIC 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 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 MG MG B 13 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 22 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 33 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 23 LIES ON A SPECIAL POSITION. 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 MG A 14 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OMG A 2 OP1 REMARK 620 2 HOH A 53 O 80.2 REMARK 620 3 HOH A 55 O 95.7 95.2 REMARK 620 4 HOH A 57 O 160.8 116.9 75.0 REMARK 620 5 HOH A 54 O 92.9 148.4 116.2 76.9 REMARK 620 6 HOH A 56 O 78.1 91.2 170.2 108.6 57.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 13 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OMC B 11 OP1 REMARK 620 2 HOH B 16 O 89.9 REMARK 620 3 HOH B 15 O 90.8 89.3 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 MG B 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 14 DBREF 310D A 1 6 PDB 310D 310D 1 6 DBREF 310D B 7 12 PDB 310D 310D 7 12 SEQRES 1 A 6 OMC OMG OMC OMG OMC OMG SEQRES 1 B 6 OMC OMG OMC OMG OMC OMG MODRES 310D OMC A 1 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 310D OMG A 2 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 310D OMC A 3 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 310D OMG A 4 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 310D OMC A 5 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 310D OMG A 6 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 310D OMC B 7 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 310D OMG B 8 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 310D OMC B 9 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 310D OMG B 10 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 310D OMC B 11 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 310D OMG B 12 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HET OMC A 1 29 HET OMG A 2 37 HET OMC A 3 34 HET OMG A 4 37 HET OMC A 5 34 HET OMG A 6 37 HET OMC B 7 31 HET OMG B 8 37 HET OMC B 9 34 HET OMG B 10 37 HET OMC B 11 34 HET OMG B 12 37 HET MG A 14 1 HET MG B 13 1 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 OMC 6(C10 H16 N3 O8 P) FORMUL 1 OMG 6(C11 H16 N5 O8 P) FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *44(H2 O) LINK O3' OMC A 1 P OMG A 2 1555 1555 1.62 LINK O3' OMG A 2 P OMC A 3 1555 1555 1.60 LINK O3' OMC A 3 P OMG A 4 1555 1555 1.63 LINK O3' OMG A 4 P OMC A 5 1555 1555 1.62 LINK O3' OMC A 5 P OMG A 6 1555 1555 1.58 LINK O3' OMC B 7 P OMG B 8 1555 1555 1.61 LINK O3' OMG B 8 P OMC B 9 1555 1555 1.64 LINK O3' OMC B 9 P OMG B 10 1555 1555 1.62 LINK O3' OMG B 10 P OMC B 11 1555 1555 1.64 LINK O3' OMC B 11 P OMG B 12 1555 1555 1.59 LINK OP1 OMG A 2 MG MG A 14 1555 1555 2.17 LINK OP1 OMC B 11 MG MG B 13 1555 1555 2.18 LINK MG MG B 13 O HOH B 16 1555 1555 2.14 LINK MG MG B 13 O HOH B 15 1555 1555 1.94 LINK MG MG A 14 O HOH A 53 1555 1555 2.22 LINK MG MG A 14 O HOH A 55 1555 1555 2.14 LINK MG MG A 14 O HOH A 57 1555 10665 1.92 LINK MG MG A 14 O HOH A 54 1555 1555 2.32 LINK MG MG A 14 O HOH A 56 1555 1555 2.13 SITE 1 AC1 3 OMC B 11 HOH B 15 HOH B 16 SITE 1 AC2 6 OMG A 2 HOH A 53 HOH A 54 HOH A 55 SITE 2 AC2 6 HOH A 56 HOH A 57 CRYST1 26.270 26.270 160.900 90.00 90.00 120.00 P 61 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 0.038066 0.021978 0.000000 0.00000 SCALE2 0.000000 0.043955 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006215 0.00000 MASTER 257 0 14 0 0 0 3 6 0 0 0 2 END