HEADER DNA 18-OCT-02 1N1O TITLE CRYSTAL STRUCTURE OF A B-FORM DNA DUPLEX CONTAINING (L)-ALPHA- TITLE 2 THREOFURANOSYL (3'-2') NUCLEOSIDES: A FOUR-CARBON SUGAR IS EASILY TITLE 3 ACCOMMODATED INTO THE BACKBONE OF DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*(TFT)P*TP*CP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DICKERSON-DREW DODECAMER DUPLEX SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE OLIGONUCLEOTIDE SYNTHESIS WAS USED. KEYWDS B-DNA, HYDROGEN BONDING, NUCLEIC ACID ETIOLOGY, TETROSE, FOUR-CARBON KEYWDS 2 SUGAR, NUCLEIC ACID ANALOGUE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR C.J.WILDS,Z.WAWRZAK,R.KRISHNAMURTHY,A.ESCHENMOSER,M.EGLI REVDAT 7 03-APR-24 1N1O 1 REMARK REVDAT 6 14-FEB-24 1N1O 1 REMARK LINK REVDAT 5 24-JUL-19 1N1O 1 REMARK LINK REVDAT 4 11-OCT-17 1N1O 1 REMARK REVDAT 3 24-FEB-09 1N1O 1 VERSN REVDAT 2 11-DEC-02 1N1O 1 JRNL REVDAT 1 15-NOV-02 1N1O 0 JRNL AUTH C.J.WILDS,Z.WAWRZAK,R.KRISHNAMURTHY,A.ESCHENMOSER,M.EGLI JRNL TITL CRYSTAL STRUCTURE OF A B-FORM DNA DUPLEX CONTAINING JRNL TITL 2 (L)-ALPHA-THREOFURANOSYL (3'-->2') NUCLEOSIDES: A JRNL TITL 3 FOUR-CARBON SUGAR IS EASILY ACCOMMODATED INTO THE BACKBONE JRNL TITL 4 OF DNA JRNL REF J.AM.CHEM.SOC. V. 124 13716 2002 JRNL REFN ISSN 0002-7863 JRNL PMID 12431101 JRNL DOI 10.1021/JA0207807 REMARK 2 REMARK 2 RESOLUTION. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.160 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.160 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2130 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 21311 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.156 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.156 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1866 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 18649 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 484 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 197 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) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.014 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 1N1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7 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) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21311 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03700 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) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32700 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: CNS REMARK 200 STARTING MODEL: B-FORM DNA (NATIVE DICKERSON-DREW DODECAMER) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: OLIGONUCLEOTIDE, SODIUM CACODYLATE, REMARK 280 MAGNESIUM ACETATE, SPERMINE TETRAHYDROCHLORIDE, 2-METHYL-2,4- REMARK 280 PENTANEDIOL (MPD), PH 7, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 12.63850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.93000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.04000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.93000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.63850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.04000 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 DC A 1 O4' DC A 1 C1' 0.076 REMARK 500 DC A 3 C2' DC A 3 C1' -0.063 REMARK 500 DC A 3 O4' DC A 3 C1' 0.109 REMARK 500 DA A 5 O4' DA A 5 C1' 0.098 REMARK 500 DT A 8 O4' DT A 8 C1' 0.077 REMARK 500 DC A 9 C2' DC A 9 C1' -0.088 REMARK 500 DC A 9 O4' DC A 9 C1' 0.149 REMARK 500 DC A 11 C2' DC A 11 C1' -0.069 REMARK 500 DC A 11 O4' DC A 11 C1' 0.126 REMARK 500 DG A 12 C2' DG A 12 C1' -0.073 REMARK 500 DG A 12 O4' DG A 12 C1' 0.092 REMARK 500 DC B 113 O4' DC B 113 C1' 0.079 REMARK 500 DC B 115 O4' DC B 115 C1' 0.104 REMARK 500 DA B 117 C2' DA B 117 C1' -0.060 REMARK 500 DA B 117 O4' DA B 117 C1' 0.123 REMARK 500 DA B 118 O4' DA B 118 C1' 0.079 REMARK 500 DT B 120 C2' DT B 120 C1' -0.066 REMARK 500 DT B 120 O4' DT B 120 C1' 0.099 REMARK 500 DC B 121 C2' DC B 121 C1' -0.079 REMARK 500 DC B 121 O4' DC B 121 C1' 0.129 REMARK 500 DC B 123 C2' DC B 123 C1' -0.103 REMARK 500 DC B 123 O4' DC B 123 C1' 0.137 REMARK 500 DG B 124 C2' DG B 124 C1' -0.094 REMARK 500 DG B 124 O4' DG B 124 C1' 0.132 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 1 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 1 N1 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 DG A 2 OP1 - P - OP2 ANGL. DEV. = 9.2 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC A 9 N1 - C1' - C2' ANGL. DEV. = 11.9 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = -10.8 DEGREES REMARK 500 DC A 11 N1 - C1' - C2' ANGL. DEV. = 10.9 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -9.1 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = -8.1 DEGREES REMARK 500 DC B 113 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG B 114 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC B 115 O4' - C1' - N1 ANGL. DEV. = -7.3 DEGREES REMARK 500 DG B 116 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 116 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 DA B 117 O4' - C1' - N9 ANGL. DEV. = -7.2 DEGREES REMARK 500 DA B 118 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DT B 120 O5' - C5' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DT B 120 O4' - C1' - N1 ANGL. DEV. = -7.8 DEGREES REMARK 500 DC B 121 C1' - O4' - C4' ANGL. DEV. = -8.7 DEGREES REMARK 500 DC B 121 N1 - C1' - C2' ANGL. DEV. = 9.4 DEGREES REMARK 500 DC B 121 O4' - C1' - N1 ANGL. DEV. = -8.0 DEGREES REMARK 500 DC B 123 N1 - C1' - C2' ANGL. DEV. = 9.3 DEGREES REMARK 500 DC B 123 O4' - C1' - N1 ANGL. DEV. = -9.1 DEGREES REMARK 500 DG B 124 N9 - C1' - C2' ANGL. DEV. = 9.1 DEGREES REMARK 500 DG B 124 O4' - C1' - N9 ANGL. DEV. = -8.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 702 O REMARK 620 2 HOH A 705 O 92.4 REMARK 620 3 HOH B 706 O 174.8 88.6 REMARK 620 4 HOH B 708 O 94.0 86.2 91.1 REMARK 620 5 HOH B 715 O 89.9 91.5 85.1 175.5 REMARK 620 6 HOH B 720 O 88.6 174.9 90.8 88.8 93.5 REMARK 620 N 1 2 3 4 5 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 901 DBREF 1N1O A 1 12 PDB 1N1O 1N1O 1 12 DBREF 1N1O B 113 124 PDB 1N1O 1N1O 113 124 SEQRES 1 A 12 DC DG DC DG DA DA TFT DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA TFT DT DC DG DC DG MODRES 1N1O TFT A 7 DT MODRES 1N1O TFT B 119 DT HET TFT A 7 19 HET TFT B 119 19 HET MG A 901 1 HETNAM TFT (L)-ALPHA-THREOFURANOSYL-THYMINE-3'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 TFT 2(C9 H13 N2 O8 P) FORMUL 3 MG MG 2+ FORMUL 4 HOH *197(H2 O) LINK O3' DA A 6 P TFT A 7 1555 1555 1.61 LINK O2T TFT A 7 P DT A 8 1555 1555 1.61 LINK O3' DA B 118 P TFT B 119 1555 1555 1.58 LINK O2T TFT B 119 P DT B 120 1555 1555 1.55 LINK O HOH A 702 MG MG A 901 1555 1555 2.07 LINK O HOH A 705 MG MG A 901 1555 1555 2.05 LINK MG MG A 901 O HOH B 706 1555 1555 2.12 LINK MG MG A 901 O HOH B 708 1555 1555 2.06 LINK MG MG A 901 O HOH B 715 1555 1555 2.07 LINK MG MG A 901 O HOH B 720 1555 1555 2.03 SITE 1 AC1 6 HOH A 702 HOH A 705 HOH B 706 HOH B 708 SITE 2 AC1 6 HOH B 715 HOH B 720 CRYST1 25.277 40.080 65.860 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 0.039562 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024950 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015184 0.00000