10 20 30 40 50 60 70 80 2RF3 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 27-SEP-07 2RF3
TITLE CRYSTAL STRUCTURE OF TRICYCLO-DNA: AN UNUSUAL COMPENSATORY TITLE 2 CHANGE OF TWO ADJACENT BACKBONE TORSION ANGLES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(CGCG(TCY)ATTCGCG)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED MODIFIED SOURCE 4 OLIGODEOXYRIBONUCLEOTIDE (DNA)
KEYWDS DNA DUPLEX, X-RAY CRYSTAL STRUCTURE, TRICYCLO-DNA, KEYWDS 2 CONFORMATIONALLY CONSTRAINED DNA ANALOG
EXPDTA X-RAY DIFFRACTION
AUTHOR P.S.PALLAN,D.ITTIG,A.HEROUX,Z.WAWRZAK,C.J.LEUMANN,M.EGLI
REVDAT 7 10-NOV-09 2RF3 1 JRNL REVDAT 6 09-JUN-09 2RF3 1 REVDAT REVDAT 5 24-FEB-09 2RF3 1 VERSN REVDAT 4 02-DEC-08 2RF3 1 JRNL REVDAT 3 26-FEB-08 2RF3 1 JRNL REVDAT 2 19-FEB-08 2RF3 1 JRNL REVDAT 1 12-FEB-08 2RF3 0
JRNL AUTH P.S.PALLAN,D.ITTIG,A.HEROUX,Z.WAWRZAK,C.J.LEUMANN, JRNL AUTH 2 M.EGLI JRNL TITL CRYSTAL STRUCTURE OF TRICYCLO-DNA: AN UNUSUAL JRNL TITL 2 COMPENSATORY CHANGE OF TWO ADJACENT BACKBONE JRNL TITL 3 TORSION ANGLES. JRNL REF CHEM.COMMUN.(CAMB.) V.2008 883 2008 JRNL REFN ISSN 1359-7345 JRNL PMID 18253536 JRNL DOI 10.1039/B716390H
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, REFMAC 5.2.0005 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.0 REMARK 3 NUMBER OF REFLECTIONS : 6551 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) : 0.176 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 332 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.18 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 321 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE : 0.1840 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 13 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 : 492 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.33000 REMARK 3 B22 (A**2) : 0.33000 REMARK 3 B33 (A**2) : -0.50000 REMARK 3 B12 (A**2) : 0.17000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : MASK REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2RF3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-07. REMARK 100 THE RCSB ID CODE IS RCSB044780.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-07; NULL REMARK 200 TEMPERATURE (KELVIN) : 120; NULL REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; APS REMARK 200 BEAMLINE : X29A; 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.0809; NULL REMARK 200 MONOCHROMATOR : SI111; NULL REMARK 200 OPTICS : FLAT FOCUSING MIRROR; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6884 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 32.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.0 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1EHV REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.75 MM OF OLIGONUCLEOTIDE, 20 MM REMARK 280 SODIUM CACODYLATE, 6 MM NACL, 40 MM KCL AND 5% MPD AGAINST 0.7 REMARK 280 ML OF 35% MPD, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.49200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.74600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1190 ANGSTROM**2 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 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 2 O4' - C1' - N9 ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 DG B 2 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = -6.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL
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 260 DISTANCE = 5.20 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 308 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM B 309
DBREF 2RF3 A 1 12 PDB 2RF3 2RF3 1 12 DBREF 2RF3 B 1 12 PDB 2RF3 2RF3 1 12
SEQRES 1 A 12 DC DG DC DG TCY DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG TCY DA DT DT DC DG DC DG
MODRES 2RF3 TCY A 5 DA MODRES 2RF3 TCY B 5 DA
HET TCY A 5 24 HET TCY B 5 24 HET ZN B 308 1 HET SPM B 309 14
HETNAM TCY (2R,3AS,4AR,5AR,5BS)-2-(6-AMINO-9H-PURIN-9-YL)-3A- HETNAM 2 TCY HYDROXYHEXAHYDROCYCLOPROPA[4,5]CYCLOPENTA[1,2-B]FURAN- HETNAM 3 TCY 5A(4H)-YL DIHYDROGEN PHOSPHATE HETNAM ZN ZINC ION HETNAM SPM SPERMINE
FORMUL 1 TCY 2(C13 H16 N5 O6 P) FORMUL 3 ZN ZN 2+ FORMUL 4 SPM C10 H26 N4 FORMUL 5 HOH *93(H2 O)
LINK OP1 DG B 12 ZN ZN B 308 1555 1555 1.95 LINK O3' DG A 4 P TCY A 5 1555 1555 1.59 LINK O3' TCY A 5 P DA A 6 1555 1555 1.58 LINK O3' DG B 4 P TCY B 5 1555 1555 1.59 LINK O3' TCY B 5 P DA B 6 1555 1555 1.58
SITE 1 AC1 6 DC A 1 DC A 11 DG A 12 DC B 1 SITE 2 AC1 6 DC B 11 DG B 12 SITE 1 AC2 6 DG A 2 DC A 11 DG B 2 DC B 11 SITE 2 AC2 6 HOH B 257 HOH B 293
CRYST1 26.587 26.587 98.238 90.00 90.00 120.00 P 32 6
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 0.037612 0.021716 0.000000 0.00000
SCALE2 0.000000 0.043431 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010179 0.00000