HEADER DNA 01-JUL-03 1PWF TITLE ONE SUGAR PUCKER FITS ALL: PAIRING VERSATILITY DESPITE CONFORMATIONAL TITLE 2 UNIFORMITY IN TNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: A-DNA DECAMER DUPLEX WITH TNA-ADENINE AND 2'-METHOXY- COMPND 6 THYMINE MODIFICATIONS SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED OLIGONUCLEOTIDE KEYWDS A-DNA, HYDROGEN BONDING, NUCLEIC ACID ETIOLOGY, TETROSE, FOUR CARBON KEYWDS 2 SUGAR, NUCLEIC ACID ANALOGUE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PALLAN,C.J.WILDS,Z.WAWRZAK,R.KRISHNAMURTHY,A.ESCHENMOSER,M.EGLI REVDAT 5 16-AUG-23 1PWF 1 REMARK LINK REVDAT 4 24-JUL-19 1PWF 1 REMARK LINK REVDAT 3 11-OCT-17 1PWF 1 REMARK REVDAT 2 24-FEB-09 1PWF 1 VERSN REVDAT 1 13-JUL-04 1PWF 0 JRNL AUTH P.S.PALLAN,C.J.WILDS,Z.WAWRZAK,R.KRISHNAMURTHY, JRNL AUTH 2 A.ESCHENMOSER,M.EGLI JRNL TITL WHY DOES TNA CROSS-PAIR MORE STRONGLY WITH RNA THAN WITH JRNL TITL 2 DNA? AN ANSWER FROM X-RAY ANALYSIS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 42 5893 2003 JRNL REFN ESSN 0570-0833 JRNL PMID 14673929 JRNL DOI 10.1002/ANIE.200352553 REMARK 2 REMARK 2 RESOLUTION. 1.16 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.133 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 918 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 18289 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 : 406 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 109 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) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.026 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.040 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.086 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.034 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 : L. CLOWNEY ET AL., GEOMETRIC REMARK 3 PARAMETERS IN NUCLEIC ACIDS: REMARK 3 NITROGENOUS BASES, J. AM. CHEM. REMARK 3 SOC. (1996) 118, 509-518; A. REMARK 3 GELBIN ET AL., GEOMETRIC REMARK 3 PARAMETERS IN NUCLEIC ACIDS: REMARK 3 SUGAR AND PHOSPHATE CONSTITUENTS, REMARK 3 J. AM. CHEM. SOC. (1996) 118, 519- REMARK 3 529; G. PARKINSON ET AL., NEW REMARK 3 PARAMETERS FOR THE REFINEMENT OF REMARK 3 NUCLEIC ACID-CONTAINING REMARK 3 STRUCTURES, ACTA CRYST. (1996) REMARK 3 D52, 57-64. REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PWF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019634. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.0 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 : NULL 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 : SCALEPACK, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18354 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 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) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29700 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1DPL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, SODIUM CHLORIDE, REMARK 280 BARIUM CHLORIDE, SPERMINE TETRAHYDROCHLORIDE, 2-METHYL-2,4- REMARK 280 PENTANEDIOL, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291.0K 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 12.21450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.66600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.26100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.66600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.21450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.26100 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 DG A 1 C3' DG A 1 C2' -0.057 REMARK 500 DC A 2 C3' DC A 2 C2' -0.068 REMARK 500 DC A 2 C2' DC A 2 C1' -0.064 REMARK 500 DG A 3 C2' DG A 3 C1' -0.081 REMARK 500 DG A 3 O4' DG A 3 C1' 0.080 REMARK 500 DT A 4 C2' DT A 4 C1' -0.073 REMARK 500 DC B 112 C3' DC B 112 C2' -0.050 REMARK 500 DG B 119 C3' DG B 119 C2' -0.055 REMARK 500 DG B 119 C2' DG B 119 C1' -0.096 REMARK 500 DG B 119 O4' DG B 119 C1' 0.079 REMARK 500 DC B 120 C3' DC B 120 C2' -0.077 REMARK 500 DC B 120 C2' DC B 120 C1' -0.081 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 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG A 3 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -6.8 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG A 9 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG B 111 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 114 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 DA B 115 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 DG B 119 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG B 119 C4 - C5 - N7 ANGL. DEV. = -2.4 DEGREES REMARK 500 DG B 119 N3 - C2 - N2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC B 120 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC B 120 C6 - N1 - C2 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 120 C4 - C5 - C6 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC B 120 C5 - C6 - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH B 589 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N1O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A B-FORM DNA DUPLEX CONTAINING (L)-ALPHA- REMARK 900 THREOFURANOSYL (3'-->2') NUCLEOSIDES: A FOUR-CARBON SUGAR IS EASILY REMARK 900 ACCOMMODATED INTO THE BACKBONE OF DNA DBREF 1PWF A 1 10 PDB 1PWF 1PWF 1 10 DBREF 1PWF B 111 120 PDB 1PWF 1PWF 111 120 SEQRES 1 A 10 DG DC DG DT DA 2MU FA2 DC DG DC SEQRES 1 B 10 DG DC DG DT DA 2MU FA2 DC DG DC MODRES 1PWF 2MU A 6 U 2',5-DIMETHYLURIDINE-5'-MONOPHOSPHATE MODRES 1PWF FA2 A 7 DA MODRES 1PWF 2MU B 116 U 2',5-DIMETHYLURIDINE-5'-MONOPHOSPHATE MODRES 1PWF FA2 B 117 DA HET 2MU A 6 31 HET FA2 A 7 29 HET 2MU B 116 31 HET FA2 B 117 29 HET SPM B 201 14 HETNAM 2MU 2',5-DIMETHYLURIDINE-5'-MONOPHOSPHATE HETNAM FA2 5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL HETNAM 2 FA2 DIHYDROGEN PHOSPHATE HETNAM SPM SPERMINE FORMUL 1 2MU 2(C11 H17 N2 O9 P) FORMUL 1 FA2 2(C9 H12 N5 O6 P) FORMUL 3 SPM C10 H26 N4 FORMUL 4 HOH *109(H2 O) LINK O3' DA A 5 P 2MU A 6 1555 1555 1.60 LINK O3' 2MU A 6 P FA2 A 7 1555 1555 1.60 LINK O2' FA2 A 7 P DC A 8 1555 1555 1.60 LINK O3' DA B 115 P 2MU B 116 1555 1555 1.59 LINK O3' 2MU B 116 P FA2 B 117 1555 1555 1.59 LINK O2' FA2 B 117 P DC B 118 1555 1555 1.64 SITE 1 AC1 11 DG A 9 HOH A 504 HOH A 520 HOH A 521 SITE 2 AC1 11 HOH A 522 DG B 113 DT B 114 DG B 119 SITE 3 AC1 11 HOH B 534 HOH B 573 HOH B 577 CRYST1 24.429 44.522 47.332 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 0.040935 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022461 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021127 0.00000