Header list of 1xcy.pdb file
Complete list - 2 20 Bytes
HEADER DNA 03-SEP-04 1XCY
TITLE STRUCTURE OF DNA CONTAINING THE ALPHA-ANOMER OF A CARBOCYCLIC ABASIC
TITLE 2 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 PRESENT IN ALL
SOURCE 4 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 4 02-MAR-22 1XCY 1 REMARK LINK
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,F.JOHNSON
JRNL TITL IMPACT OF THE C1 CONFIGURATION OF ABASIC SITES ON DNA DUPLEX
JRNL TITL 2 STRUCTURE
JRNL REF BIOCHEMISTRY V. 43 15349 2004
JRNL REFN ISSN 0006-2960
JRNL PMID 15581347
JRNL DOI 10.1021/BI048400C
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 98, X-PLOR 3.85
REMARK 3 AUTHORS : ACCELRYS (FELIX), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 389 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 DEPOSITION ID IS D_1000030218.
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 PHOSPHATE
REMARK 210 BUFFER, 50 MM NACL, 1 MM EDTA,
REMARK 210 99.96% D2O; 1.2 MM SAMPLE, 50 MM
REMARK 210 PHOSPHATE BUFFER, 50 MM NACL, 1
REMARK 210 MM EDTA, 90% H2O, 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY, DQF-COSY, COSY45, TOCSY,
REMARK 210 NOESY, [1H-31P]HETCOR; 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 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 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. = -4.8 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. = -4.2 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 5 C3' - O3' - P ANGL. DEV. = 8.5 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. = 4.8 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 5 C3' - O3' - P ANGL. DEV. = 7.8 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
REMARK 500 THIS ENTRY HAS 317 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 HAVING THE
REMARK 900 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
MODEL 1
Complete list - 2 20 Bytes