HEADER RNA 29-APR-99 468D TITLE CRYSTAL STRUCTURE AND IMPROVED ANTISENSE PROPERTIES OF 2'-O-(2- TITLE 2 METHOXYETHYL)-RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(C43)P*(G48)P*(C43)P*(G48)P*(A44)P*(A44)P*(U36) COMPND 3 P*(U36)P*(C43)P*(G48)P*(C43)P*(G48))-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: O2* OF EACH RIBOSE MODIFIED BY METHOXYETHYL SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS 2'-O-(2-METHOXYETHYL) RIBOSE, RNA DODECAMER DUPLEX, RIBONUCLEIC ACID, KEYWDS 2 RNA EXPDTA X-RAY DIFFRACTION AUTHOR M.TEPLOVA,G.MINASOV,V.TERESHKO,G.INAMATI,P.D.COOK,M.EGLI REVDAT 6 27-FEB-13 468D 1 HETATM REVDAT 5 16-JAN-13 468D 1 HETATM REVDAT 4 16-NOV-11 468D 1 VERSN HETATM REVDAT 3 24-FEB-09 468D 1 VERSN REVDAT 2 01-APR-03 468D 1 JRNL REVDAT 1 12-MAY-99 468D 0 JRNL AUTH M.TEPLOVA,G.MINASOV,V.TERESHKO,G.B.INAMATI,P.D.COOK, JRNL AUTH 2 M.MANOHARAN,M.EGLI JRNL TITL CRYSTAL STRUCTURE AND IMPROVED ANTISENSE PROPERTIES OF JRNL TITL 2 2'-O-(2-METHOXYETHYL)-RNA. JRNL REF NAT.STRUCT.BIOL. V. 6 535 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10360355 JRNL DOI 10.1038/9304 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 5532 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 602 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 111 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.64 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 468D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-98 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9780 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 6889 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROPLETS CONTAINING 2MM REMARK 280 OLIGONUCLEOTIDE, 50 MM MGCL2, 50 MM NA HEPES PH 7.5, 15% PEG 400, REMARK 280 AGAINST 1 ML OF RESERVOIR SOLUTION CONTAINING 100 MM MGCL2, 100 REMARK 280 MM NA HEPES PH 7.5, 30% PEG 400, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 20.66000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.27500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 20.66000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.27500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 A 100 LIES ON A SPECIAL POSITION. REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 180 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH B 187 DISTANCE = 7.60 ANGSTROMS REMARK 525 HOH B 188 DISTANCE = 8.70 ANGSTROMS REMARK 525 HOH B 195 DISTANCE = 10.88 ANGSTROMS REMARK 525 HOH B 199 DISTANCE = 7.91 ANGSTROMS REMARK 525 HOH B 201 DISTANCE = 6.73 ANGSTROMS 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 100 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 102 O REMARK 620 2 HOH A 103 O 91.2 REMARK 620 3 HOH A 101 O 94.8 98.9 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 A 100 DBREF 468D A 1 12 PDB 468D 468D 1 12 DBREF 468D B 13 24 PDB 468D 468D 13 24 SEQRES 1 A 12 C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48 SEQRES 1 B 12 C43 G48 C43 G48 A44 A44 U36 U36 C43 G48 C43 G48 MODRES 468D C43 A 1 C MODRES 468D G48 A 2 G MODRES 468D C43 A 3 C MODRES 468D G48 A 4 G MODRES 468D A44 A 5 A MODRES 468D A44 A 6 A MODRES 468D U36 A 7 U MODRES 468D U36 A 8 U MODRES 468D C43 A 9 C MODRES 468D G48 A 10 G MODRES 468D C43 A 11 C MODRES 468D G48 A 12 G MODRES 468D C43 B 13 C MODRES 468D G48 B 14 G MODRES 468D C43 B 15 C MODRES 468D G48 B 16 G MODRES 468D A44 B 17 A MODRES 468D A44 B 18 A MODRES 468D U36 B 19 U MODRES 468D U36 B 20 U MODRES 468D C43 B 21 C MODRES 468D G48 B 22 G MODRES 468D C43 B 23 C MODRES 468D G48 B 24 G HET C43 A 1 21 HET G48 A 2 27 HET C43 A 3 24 HET G48 A 4 27 HET A44 A 5 26 HET A44 A 6 26 HET U36 A 7 24 HET U36 A 8 24 HET C43 A 9 24 HET G48 A 10 27 HET C43 A 11 24 HET G48 A 12 27 HET C43 B 13 21 HET G48 B 14 27 HET C43 B 15 24 HET G48 B 16 27 HET A44 B 17 26 HET A44 B 18 26 HET U36 B 19 24 HET U36 B 20 24 HET C43 B 21 24 HET G48 B 22 27 HET C43 B 23 24 HET G48 B 24 27 HET MG A 100 1 HETNAM C43 2'-O-METHYOXYETHYL-CYTIDINE-5'-MONOPHOSPHATE HETNAM G48 2'-O-METHYOXYETHYL-GUANOSINE-5'-MONOPHOSPHATE HETNAM A44 2'-O-METHYOXYETHYL-ADENOSINE 5'-MONOPHOSPHATE HETNAM U36 2'-O-METHYOXYETHYL-URIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 C43 8(C12 H20 N3 O9 P) FORMUL 1 G48 8(C13 H20 N5 O9 P) FORMUL 1 A44 4(C13 H20 N5 O8 P) FORMUL 1 U36 4(C12 H19 N2 O10 P) FORMUL 3 MG MG 2+ FORMUL 4 HOH *111(H2 O) LINK MG MG A 100 O HOH A 102 1555 1555 2.27 LINK O HOH A 103 MG MG A 100 1555 2656 2.03 LINK O HOH A 101 MG MG A 100 1555 2656 1.98 LINK O3' C43 A 1 P G48 A 2 1555 1555 1.62 LINK O3' G48 A 2 P C43 A 3 1555 1555 1.60 LINK O3' C43 A 3 P G48 A 4 1555 1555 1.61 LINK O3' G48 A 4 P A44 A 5 1555 1555 1.59 LINK O3' A44 A 5 P A44 A 6 1555 1555 1.61 LINK O3' A44 A 6 P U36 A 7 1555 1555 1.60 LINK O3' U36 A 7 P U36 A 8 1555 1555 1.61 LINK O3' U36 A 8 P C43 A 9 1555 1555 1.62 LINK O3' C43 A 9 P G48 A 10 1555 1555 1.60 LINK O3' G48 A 10 P C43 A 11 1555 1555 1.60 LINK O3' C43 A 11 P G48 A 12 1555 1555 1.60 LINK O3' C43 B 13 P G48 B 14 1555 1555 1.59 LINK O3' G48 B 14 P C43 B 15 1555 1555 1.60 LINK O3' C43 B 15 P G48 B 16 1555 1555 1.61 LINK O3' G48 B 16 P A44 B 17 1555 1555 1.62 LINK O3' A44 B 17 P A44 B 18 1555 1555 1.61 LINK O3' A44 B 18 P U36 B 19 1555 1555 1.61 LINK O3' U36 B 19 P U36 B 20 1555 1555 1.61 LINK O3' U36 B 20 P C43 B 21 1555 1555 1.60 LINK O3' C43 B 21 P G48 B 22 1555 1555 1.61 LINK O3' G48 B 22 P C43 B 23 1555 1555 1.60 LINK O3' C43 B 23 P G48 B 24 1555 1555 1.60 LINK MG MG A 100 O HOH A 103 1555 1555 2.05 LINK MG MG A 100 O HOH A 101 1555 1555 2.00 SITE 1 AC1 3 HOH A 101 HOH A 102 HOH A 103 CRYST1 41.320 34.550 46.600 90.00 92.30 90.00 C 1 2 1 8 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 0.024201 0.000000 0.000972 0.00000 SCALE2 0.000000 0.028944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021477 0.00000 MASTER 244 0 25 0 0 0 1 6 0 0 0 2 END