10 20 30 40 50 60 70 80 1XCY - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 03-SEP-04 1XCY
TITLE STRUCTURE OF DNA CONTAINING THE ALPHA-ANOMER OF A TITLE 2 CARBOCYCLIC ABASIC SITE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*TP*AP*CP*(DXD)P*CP*AP*TP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*AP*TP*GP*AP*GP*TP*AP*CP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: APYRIMIDINIC ABASIC SITES ARE NORMALLY SOURCE 4 PRESENT IN ALL GENOMES; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES
KEYWDS DOUBLE HELIX, ABASIC SITE, DNA
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR C.DE LOS SANTOS,M.EL-KHATEEB,P.REGE,K.TIAN,F.JOHNSON
REVDAT 3 24-FEB-09 1XCY 1 VERSN REVDAT 2 21-DEC-04 1XCY 1 JRNL REVDAT 1 19-OCT-04 1XCY 0
JRNL AUTH C.DE LOS SANTOS,M.EL-KHATEEB,P.REGE,K.TIAN, JRNL AUTH 2 F.JOHNSON JRNL TITL IMPACT OF THE C1 CONFIGURATION OF ABASIC SITES ON JRNL TITL 2 DNA DUPLEX STRUCTURE JRNL REF BIOCHEMISTRY V. 43 15349 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15581347 JRNL DOI 10.1021/BI048400C
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.85 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 389 DISTANCES BETWEEN NON-EXCHANGEABLE PROTONS, 26 DISTANCE REMARK 3 RESTRAINTS ENFORCING WC BASE PAIRS AND 96 BACKBONE DIHEDRAL REMARK 3 RESTRAINTS.
REMARK 4 REMARK 4 1XCY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-04. REMARK 100 THE RCSB ID CODE IS RCSB030218.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290; 277 REMARK 210 PH : 6.9; 6.9 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM SAMPLE, 50 MM REMARK 210 PHOSPHATE BUFFER, 50 MM NACL, REMARK 210 1 MM EDTA, 99.96% D2O; 1.2 MM REMARK 210 SAMPLE, 50 MM PHOSPHATE REMARK 210 BUFFER, 50 MM NACL, 1 MM EDTA, REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY, DQF-COSY, COSY45, REMARK 210 TOCSY, NOESY, [1H-31P]HETCOR, REMARK 210 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98, VNMR 6.1, CURVES 5.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : CONVERGING STRUCTURES (<1.5A) REMARK 210 AND THOSE WITH THE LEAST REMARK 210 RESTRAINTS VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SEVERAL NOESY SPECTRA RECORDED USING DIFFERENT MIXING REMARK 210 TIMES.
REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.
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 1 DC A 1 C4 DC A 1 N4 0.096 REMARK 500 1 DG A 2 C2 DG A 2 N2 0.083 REMARK 500 1 DT A 3 C5 DT A 3 C7 0.039 REMARK 500 1 DA A 4 C3' DA A 4 C2' 0.081 REMARK 500 1 DA A 4 C6 DA A 4 N6 0.097 REMARK 500 1 DC A 5 C4 DC A 5 N4 0.095 REMARK 500 1 DC A 7 C3' DC A 7 C2' 0.093 REMARK 500 1 DC A 7 C2' DC A 7 C1' 0.073 REMARK 500 1 DC A 7 C4 DC A 7 N4 0.095 REMARK 500 1 DC A 7 N1 DC A 7 C6 0.050 REMARK 500 1 DA A 8 C2' DA A 8 C1' 0.097 REMARK 500 1 DA A 8 C6 DA A 8 N6 0.091 REMARK 500 1 DT A 9 C5 DT A 9 C7 0.036 REMARK 500 1 DG A 10 C2 DG A 10 N2 0.084 REMARK 500 1 DC A 11 C4 DC A 11 N4 0.096 REMARK 500 1 DG B 12 C2 DG B 12 N2 0.082 REMARK 500 1 DC B 13 C4 DC B 13 N4 0.095 REMARK 500 1 DA B 14 C2' DA B 14 C1' 0.178 REMARK 500 1 DA B 14 C6 DA B 14 N6 0.095 REMARK 500 1 DT B 15 C3' DT B 15 C2' 0.122 REMARK 500 1 DT B 15 C2' DT B 15 C1' 0.077 REMARK 500 1 DT B 15 C5 DT B 15 C7 0.036 REMARK 500 1 DG B 16 C2 DG B 16 N2 0.084 REMARK 500 1 DA B 17 C6 DA B 17 N6 0.097 REMARK 500 1 DG B 18 C4' DG B 18 C3' 0.091 REMARK 500 1 DG B 18 C3' DG B 18 C2' 0.078 REMARK 500 1 DG B 18 C2 DG B 18 N2 0.079 REMARK 500 1 DT B 19 C5 DT B 19 C7 0.037 REMARK 500 1 DA B 20 C3' DA B 20 C2' 0.082 REMARK 500 1 DA B 20 C6 DA B 20 N6 0.097 REMARK 500 1 DC B 21 C4 DC B 21 N4 0.096 REMARK 500 1 DG B 22 C2 DG B 22 N2 0.089 REMARK 500 2 DC A 1 C4 DC A 1 N4 0.095 REMARK 500 2 DG A 2 C2 DG A 2 N2 0.083 REMARK 500 2 DT A 3 C5 DT A 3 C7 0.039 REMARK 500 2 DA A 4 C3' DA A 4 C2' 0.084 REMARK 500 2 DA A 4 C6 DA A 4 N6 0.097 REMARK 500 2 DC A 5 C4 DC A 5 N4 0.096 REMARK 500 2 DC A 7 C3' DC A 7 C2' 0.091 REMARK 500 2 DC A 7 C2' DC A 7 C1' 0.070 REMARK 500 2 DC A 7 C4 DC A 7 N4 0.095 REMARK 500 2 DC A 7 N1 DC A 7 C6 0.048 REMARK 500 2 DA A 8 C2' DA A 8 C1' 0.097 REMARK 500 2 DA A 8 C6 DA A 8 N6 0.092 REMARK 500 2 DT A 9 C5 DT A 9 C7 0.036 REMARK 500 2 DG A 10 C2 DG A 10 N2 0.082 REMARK 500 2 DC A 11 C4 DC A 11 N4 0.097 REMARK 500 2 DG B 12 C2 DG B 12 N2 0.083 REMARK 500 2 DC B 13 C4 DC B 13 N4 0.095 REMARK 500 2 DA B 14 C2' DA B 14 C1' 0.177 REMARK 500 REMARK 500 THIS ENTRY HAS 282 BOND DEVIATIONS. 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 1 DC A 1 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 4 O4' - C4' - C3' ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DA A 4 C4' - C3' - C2' ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DA A 4 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DA A 4 O4' - C1' - C2' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DC A 7 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DC A 7 C4' - C3' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DC A 7 O4' - C1' - C2' ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DC A 7 N1 - C1' - C2' ANGL. DEV. = 15.0 DEGREES REMARK 500 1 DC A 7 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DC A 7 C6 - N1 - C1' ANGL. DEV. = 9.8 DEGREES REMARK 500 1 DC A 7 C2 - N1 - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DA A 8 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 10 C3' - C2' - C1' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC A 11 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA B 14 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DA B 14 O4' - C1' - C2' ANGL. DEV. = -12.0 DEGREES REMARK 500 1 DT B 15 C3' - C2' - C1' ANGL. DEV. = -8.5 DEGREES REMARK 500 1 DT B 15 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA B 20 O4' - C4' - C3' ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DA B 20 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DA B 20 C3' - C2' - C1' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DA B 20 O4' - C1' - C2' ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA B 20 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 21 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG B 22 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 4 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DA A 4 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DA A 4 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DA A 4 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DC A 7 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 7 C4' - C3' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 2 DC A 7 O4' - C1' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 2 DC A 7 N1 - C1' - C2' ANGL. DEV. = 14.8 DEGREES REMARK 500 2 DC A 7 C6 - N1 - C1' ANGL. DEV. = 10.0 DEGREES REMARK 500 2 DC A 7 C2 - N1 - C1' ANGL. DEV. = -7.5 DEGREES REMARK 500 2 DA A 8 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 309 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
REMARK 600 REMARK 600 HETEROGEN REMARK 600 SUGAR PROTONS IDENTIFIED WITH ASTERISKS IN THE REMARK 600 COORDINATE FILE ARE NAMED WITH PRIMES IN THE REMARK 600 PRIMARY CITATION.
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XCZ RELATED DB: PDB REMARK 900 STRUCTURE OF A RELATED DUPLEX OF IDENTICAL SEQUENCE BUT REMARK 900 HAVING THE BETA-ANOMER OF THE CARBOCYCLIC ABASIC SITE
DBREF 1XCY A 1 11 PDB 1XCY 1XCY 1 11 DBREF 1XCY B 12 22 PDB 1XCY 1XCY 12 22
SEQRES 1 A 11 DC DG DT DA DC DXD DC DA DT DG DC SEQRES 1 B 11 DG DC DA DT DG DA DG DT DA DC DG
HET DXD A 6 22
HETNAM DXD (1S,3S,4R)-4-(PHOSPHOOXYMETHYL)-CYCLOPENTANE-1,3-DIOL
FORMUL 1 DXD C6 H13 O6 P
LINK O3' DC A 5 P DXD A 6 1555 1555 1.61 LINK O3' DXD A 6 P DC A 7 1555 1555 1.62
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000