HEADER DNA 04-SEP-05 2AXB TITLE CRYSTAL STRUCTURE ANALYSIS OF A 2-O-[2-(METHOXY)ETHYL]-2-THIOTHYMIDINE TITLE 2 MODIFIED OLIGODEOXYNUCLEOTIDE DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(S2M)P*AP*CP*GP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA EXPDTA X-RAY DIFFRACTION AUTHOR B.DIOP-FRIMPONG,T.P.PRAKASH,K.G.RAJEEV,M.MANOHARAN,M.EGLI REVDAT 4 14-FEB-24 2AXB 1 LINK REVDAT 3 11-OCT-17 2AXB 1 REMARK REVDAT 2 24-FEB-09 2AXB 1 VERSN REVDAT 1 01-NOV-05 2AXB 0 JRNL AUTH B.DIOP-FRIMPONG,T.P.PRAKASH,K.G.RAJEEV,M.MANOHARAN,M.EGLI JRNL TITL STABILIZING CONTRIBUTIONS OF SULFUR-MODIFIED NUCLEOTIDES: JRNL TITL 2 CRYSTAL STRUCTURE OF A DNA DUPLEX WITH JRNL TITL 3 2'-O-[2-(METHOXY)ETHYL]-2-THIOTHYMIDINES. JRNL REF NUCLEIC ACIDS RES. V. 33 5297 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 16170156 JRNL DOI 10.1093/NAR/GKI823 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 6304 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 + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 338 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 414 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1170 REMARK 3 BIN FREE R VALUE SET COUNT : 22 REMARK 3 BIN FREE R VALUE : 0.1380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 414 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.08000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.232 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.209 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.872 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 463 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 198 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 694 ; 2.534 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 498 ; 1.629 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 62 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 218 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 2 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 122 ; 0.331 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 245 ; 0.373 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 91 ; 0.200 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 138 ; 0.321 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 1 ; 0.091 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 33 ; 0.195 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.343 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 463 ; 3.703 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 690 ; 4.235 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 463 ; 2.856 ; 1.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 160 ;17.014 ; 9.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 414 ; 4.893 ; 9.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2AXB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : .9873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6642 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 12.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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: 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 (%): 37.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MINI SCREEN, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 287K 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 12.62550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.48550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.50100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.48550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.62550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.50100 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 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 DA B 17 O3' DA B 17 C3' -0.042 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 DC A 2 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC A 2 C6 - N1 - C2 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DA A 5 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 S2M A 6 O3' - P - OP2 ANGL. DEV. = 13.7 DEGREES REMARK 500 S2M A 6 C3' - O3' - P ANGL. DEV. = -47.5 DEGREES REMARK 500 DA A 7 O3' - P - OP2 ANGL. DEV. = 44.5 DEGREES REMARK 500 DA A 7 O3' - P - OP1 ANGL. DEV. = -23.2 DEGREES REMARK 500 DA A 7 OP1 - P - OP2 ANGL. DEV. = -11.2 DEGREES REMARK 500 DG A 9 O4' - C4' - C3' ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 9 C5 - C6 - O6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DC B 12 O4' - C4' - C3' ANGL. DEV. = -4.1 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC B 12 N3 - C4 - N4 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT B 14 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DT B 14 N3 - C4 - O4 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 15 C3' - O3' - P ANGL. DEV. = -8.2 DEGREES REMARK 500 S2M B 16 O3' - P - OP1 ANGL. DEV. = 7.6 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 20 C5 - C4 - N4 ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2AXB A 1 10 PDB 2AXB 2AXB 1 10 DBREF 2AXB B 11 20 PDB 2AXB 2AXB 11 20 SEQRES 1 A 10 DG DC DG DT DA S2M DA DC DG DC SEQRES 1 B 10 DG DC DG DT DA S2M DA DC DG DC MODRES 2AXB S2M A 6 DT MODRES 2AXB S2M B 16 DT HET S2M A 6 25 HET S2M B 16 25 HETNAM S2M 2'-O-[2-(METHOXY)ETHYL]-2-THIOTHYMIDINE-5'- HETNAM 2 S2M MONOPHOSPHATE FORMUL 1 S2M 2(C13 H21 N2 O9 P S) FORMUL 3 HOH *154(H2 O) LINK O3' DA A 5 P S2M A 6 1555 1555 1.57 LINK C3' S2M A 6 P DA A 7 1555 1555 1.78 LINK O3' S2M A 6 P DA A 7 1555 1555 1.59 LINK O3' S2M A 6 OP1 DA A 7 1555 1555 2.02 LINK O3' DA B 15 P S2M B 16 1555 1555 1.61 LINK O3' S2M B 16 P DA B 17 1555 1555 1.59 CRYST1 25.251 45.002 44.971 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 0.039602 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022237 0.00000