HEADER DNA 31-AUG-02 1MLX TITLE CRYSTAL STRUCTURE ANALYSIS OF A 2'-O-[2-(METHYLTHIO)-ETHYL]-MODIFIED TITLE 2 OLIGODEOXYNUCLEOTIDE DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*SMTP*AP*CP*GP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SELF-COMPLEMENTARY DNA DECAMER WITH A 2'-O-[2- COMPND 6 (METHYLTHIO)ETHYL]-MODIFIED THYMINE (SMT) AT POSITION 6 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE OLIGONUCLEOTIDE SYNTHESIS KEYWDS DNA, DOUBLE HELIX, A-FORM, ANTISENSE MODIFICATION, NUCLEIC ACID KEYWDS 2 ANALOGUE, RNA AFFINITY, NUCLEASE RESISTANCE, PROTEIN BINDING KEYWDS 3 AFFINITY, HIGH RESOLUTION STRUCTURE, HYDRATION EXPDTA X-RAY DIFFRACTION AUTHOR T.P.PRAKASH,M.MANOHARAN,A.M.KAWASAKI,A.S.FRASER,E.A.LESNIK,N.SIOUFI, AUTHOR 2 J.M.LEEDS,M.TEPLOVA,M.EGLI REVDAT 4 14-FEB-24 1MLX 1 LINK REVDAT 3 11-OCT-17 1MLX 1 REMARK REVDAT 2 24-FEB-09 1MLX 1 VERSN REVDAT 1 04-DEC-02 1MLX 0 JRNL AUTH T.P.PRAKASH,M.MANOHARAN,A.M.KAWASAKI,A.S.FRASER,E.A.LESNIK, JRNL AUTH 2 N.SIOUFI,J.M.LEEDS,M.TEPLOVA,M.EGLI JRNL TITL 2'-O-[2-(METHYLTHIO)ETHYL]-MODIFIED OLIGONUCLEOTIDE: AN JRNL TITL 2 ANALOGUE OF 2'-O-[2-(METHOXY)-ETHYL]-MODIFIED JRNL TITL 3 OLIGONUCLEOTIDE WITH IMPROVED PROTEIN BINDING PROPERTIES AND JRNL TITL 4 HIGH BINDING AFFINITY TO TARGET RNA JRNL REF BIOCHEMISTRY V. 41 11642 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12269806 JRNL DOI 10.1021/BI020264T REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL 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) : 0.141 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.137 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) : 14054 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)) : NULL 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)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 411 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 146 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.029 REMARK 3 ANGLE DISTANCES (A) : 0.034 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MLX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017004. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.0 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) : 1.0000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12796 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 36.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, POTASSIUM CHLORIDE, REMARK 280 SPERMINE TETRAHYDROCHLORIDE, 2-METHYL-2,4-PENTANEDIOL (MPD), PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 12.36400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.11450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.23650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.11450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.36400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.23650 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 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 SMT A 6 CB SC CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 793 O HOH A 864 1.96 REMARK 500 O HOH B 775 O HOH B 822 2.09 REMARK 500 O HOH B 777 O HOH B 863 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC A 2 C4 DC A 2 C5 0.050 REMARK 500 DG A 3 O4' DG A 3 C1' 0.082 REMARK 500 DT A 4 C5 DT A 4 C7 -0.047 REMARK 500 DA A 5 N1 DA A 5 C2 0.059 REMARK 500 DA A 7 C6 DA A 7 N1 -0.044 REMARK 500 DC A 8 C4 DC A 8 N4 -0.060 REMARK 500 DC A 8 C5 DC A 8 C6 -0.064 REMARK 500 DG A 9 C6 DG A 9 N1 0.048 REMARK 500 DC A 10 C2 DC A 10 O2 -0.056 REMARK 500 DC A 10 C2 DC A 10 N3 0.050 REMARK 500 DG B 111 N3 DG B 111 C4 -0.046 REMARK 500 DG B 111 C8 DG B 111 N9 0.062 REMARK 500 DG B 113 C2 DG B 113 N3 -0.048 REMARK 500 DT B 114 C5 DT B 114 C6 -0.069 REMARK 500 DA B 115 N1 DA B 115 C2 -0.070 REMARK 500 DA B 117 C6 DA B 117 N1 0.046 REMARK 500 DA B 117 N7 DA B 117 C8 0.046 REMARK 500 DG B 119 C2' DG B 119 C1' -0.067 REMARK 500 DG B 119 C5 DG B 119 N7 0.039 REMARK 500 DC B 120 C4 DC B 120 C5 0.050 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG A 1 C6 - N1 - C2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 1 N1 - C2 - N3 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG A 1 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 1 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG A 3 C6 - N1 - C2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 3 N1 - C2 - N3 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG A 3 C2 - N3 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA A 5 N1 - C2 - N3 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA A 5 C5 - N7 - C8 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 5 N7 - C8 - N9 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA A 7 C6 - N1 - C2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 8 O4' - C4' - C3' ANGL. DEV. = -3.7 DEGREES REMARK 500 DG A 9 O4' - C1' - C2' ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 9 C6 - N1 - C2 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A 9 N1 - C2 - N3 ANGL. DEV. = 7.8 DEGREES REMARK 500 DG A 9 N3 - C2 - N2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG A 9 N1 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 9 C5 - C6 - O6 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 111 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG B 111 N1 - C2 - N3 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG B 111 C2 - N3 - C4 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG B 111 C6 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC B 112 C6 - N1 - C2 ANGL. DEV. = -5.7 DEGREES REMARK 500 DC B 112 C4 - C5 - C6 ANGL. DEV. = -4.1 DEGREES REMARK 500 DC B 112 C5 - C6 - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DG B 113 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 DG B 113 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG B 113 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DT B 114 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DT B 114 C5 - C6 - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA B 117 C8 - N9 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 117 N9 - C4 - C5 ANGL. DEV. = -2.4 DEGREES REMARK 500 DG B 119 P - O5' - C5' ANGL. DEV. = 10.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1MLX A 1 10 PDB 1MLX 1MLX 1 10 DBREF 1MLX B 111 120 PDB 1MLX 1MLX 111 120 SEQRES 1 A 10 DG DC DG DT DA SMT DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA SMT DA DC DG DC MODRES 1MLX SMT A 6 T MODRES 1MLX SMT B 116 T HET SMT A 6 32 HET SMT B 116 35 HETNAM SMT 2'-[(METHYLTHIO)ETHYLOXY]-THYMIDINE-5'-MONOPHOSPHATE FORMUL 1 SMT 2(C13 H21 N2 O9 P S) FORMUL 3 HOH *146(H2 O) LINK O3' DA A 5 P SMT A 6 1555 1555 1.61 LINK O3' SMT A 6 P DA A 7 1555 1555 1.61 LINK O3' DA B 115 P SMT B 116 1555 1555 1.60 LINK O3' SMT B 116 P DA B 117 1555 1555 1.62 CRYST1 24.728 44.473 46.229 90.00 90.00 90.00 P 21 21 21 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 0.040440 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022486 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021631 0.00000