Header list of 1idx.pdb file
Complete list - 23 20 Bytes
HEADER DNA 05-APR-01 1IDX
TITLE STRUCTURAL BASIS FOR POOR EXCISION FROM HAIRPIN DNA: NMR STUDY
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*UP*TP*GP*GP*AP*TP*CP*CP*T)
COMPND 3 -3';
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: URACIL CONTAINING HAIRPIN DNA
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CUSTOM MADE BY RANSOM HILL BIOSCIENCES, INC., RAMONA
SOURCE 4 CA (USA)
KEYWDS URACIL, HAIRPIN DNA, HAIRPIN LOOP, DOUBLE HELIX, UDG-URACIL
KEYWDS 2 INTERACTION, DNA
EXPDTA SOLUTION NMR
NUMMDL 6
AUTHOR M.GHOSH,N.RUMPAL,U.VARSHNEY,K.V.CHARY
REVDAT 4 23-FEB-22 1IDX 1 REMARK
REVDAT 3 24-FEB-09 1IDX 1 VERSN
REVDAT 2 01-APR-03 1IDX 1 JRNL
REVDAT 1 08-MAY-02 1IDX 0
JRNL AUTH M.GHOSH,N.RUMPAL,U.VARSHNEY,K.V.CHARY
JRNL TITL STRUCTURAL BASIS FOR POOR URACIL EXCISION FROM HAIRPIN DNA.
JRNL TITL 2 AN NMR STUDY.
JRNL REF EUR.J.BIOCHEM. V. 269 1886 2002
JRNL REFN ISSN 0014-2956
JRNL PMID 11952790
JRNL DOI 10.1046/J.1432-1033.2002.02837.X
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1, DISCOVER 97
REMARK 3 AUTHORS : VARIAN (VNMR), MSI (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 196 RESTRAINTS, 122 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 64
REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 10 DISTANCE RESTRAINTS FROM HYDROGEN
REMARK 3 BONDS.
REMARK 4
REMARK 4 1IDX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-01.
REMARK 100 THE DEPOSITION ID IS D_1000013191.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 305; 295
REMARK 210 PH : 7.0; 7.0
REMARK 210 IONIC STRENGTH : NULL; NULL
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 2 MM OLIGO; NO BUFFER; PH = 7.0;
REMARK 210 305K; 99% D2O; 2 MM OLIGO; NO
REMARK 210 BUFFER; PH = 7.0; 305K; 90% H2O +
REMARK 210 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; E-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS; AMX
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : DISCOVER 97, VNMR 6.1, UXNMR
REMARK 210 3.0, FELIX 97
REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS
REMARK 210 AND ENERGY MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY,STRUCTURES
REMARK 210 WITH FAVORABLE NON-BOND ENERGY,
REMARK 210 STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR
REMARK 210 TECHNIQUES
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 DU A 1B N1 DU A 1B C6 0.102
REMARK 500 2 DU A 1B N1 DU A 1B C6 0.103
REMARK 500 3 DU A 1B N1 DU A 1B C6 0.103
REMARK 500 4 DU A 1B N1 DU A 1B C6 0.101
REMARK 500 5 DU A 1B N1 DU A 1B C6 0.102
REMARK 500 6 DU A 1B N1 DU A 1B C6 0.103
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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES
REMARK 500 1 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DA A 1 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES
REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DT A 8 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DT A 8 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES
REMARK 500 1 DT A 9 C6 - N1 - C2 ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DT A 9 C2 - N3 - C4 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 DT A 9 C5 - C6 - N1 ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 DT A 9 C6 - N1 - C1' ANGL. DEV. = 10.6 DEGREES
REMARK 500 1 DU A 1B O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DU A 1B N1 - C2 - N3 ANGL. DEV. = 5.7 DEGREES
REMARK 500 1 DU A 1B N3 - C2 - O2 ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DT A 2B O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 2B N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 1 DT A 2B C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DG A 3B O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 1 DG A 3B O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES
REMARK 500 1 DG A 4B O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DA A 5B O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 1 DA A 5B C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DT A 6B O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 6B N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DT A 6B C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 DC A 7B O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DC A 8B O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES
REMARK 500 1 DT A 9B N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DT A 9B C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES
REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES
REMARK 500 2 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DA A 1 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES
REMARK 500 2 DG A 2 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES
REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES
REMARK 500 2 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 223 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 DG A 2 0.08 SIDE CHAIN
REMARK 500 1 DT A 8 0.09 SIDE CHAIN
REMARK 500 1 DT A 9 0.42 SIDE CHAIN
REMARK 500 1 DT A 2B 0.07 SIDE CHAIN
REMARK 500 1 DG A 3B 0.06 SIDE CHAIN
REMARK 500 2 DG A 2 0.07 SIDE CHAIN
REMARK 500 2 DT A 8 0.09 SIDE CHAIN
REMARK 500 2 DT A 9 0.40 SIDE CHAIN
REMARK 500 2 DT A 2B 0.15 SIDE CHAIN
REMARK 500 2 DG A 3B 0.06 SIDE CHAIN
REMARK 500 3 DA A 1 0.06 SIDE CHAIN
REMARK 500 3 DG A 2 0.06 SIDE CHAIN
REMARK 500 3 DT A 8 0.08 SIDE CHAIN
REMARK 500 3 DT A 9 0.43 SIDE CHAIN
REMARK 500 3 DT A 2B 0.07 SIDE CHAIN
REMARK 500 4 DG A 2 0.08 SIDE CHAIN
REMARK 500 4 DT A 8 0.09 SIDE CHAIN
REMARK 500 4 DT A 9 0.41 SIDE CHAIN
REMARK 500 4 DT A 2B 0.08 SIDE CHAIN
REMARK 500 4 DG A 3B 0.07 SIDE CHAIN
REMARK 500 4 DT A 6B 0.08 SIDE CHAIN
REMARK 500 5 DG A 2 0.08 SIDE CHAIN
REMARK 500 5 DT A 8 0.09 SIDE CHAIN
REMARK 500 5 DT A 9 0.42 SIDE CHAIN
REMARK 500 5 DT A 2B 0.07 SIDE CHAIN
REMARK 500 5 DG A 3B 0.06 SIDE CHAIN
REMARK 500 6 DG A 2 0.07 SIDE CHAIN
REMARK 500 6 DT A 8 0.09 SIDE CHAIN
REMARK 500 6 DT A 9 0.40 SIDE CHAIN
REMARK 500 6 DT A 2B 0.15 SIDE CHAIN
REMARK 500 6 DG A 3B 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1II1 RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS FOR POOR URACIL EXCISION FROM HAIRPIN DNA: NMR
REMARK 900 STUDY
REMARK 900 RELATED ID: 1QE7 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA.
REMARK 900 RELATED ID: 1DGO RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS FOR URACIL DNA GLYCOSYLASE INTERACTION WITH URACIL:
REMARK 900 NMR STUDY
REMARK 900 RELATED ID: 4536 RELATED DB: BMRB
REMARK 900 STRUCTURAL BASIS FOR URACIL DNA GLYCOSYLASE INTERACTION WITH URACIL:
REMARK 900 NMR STUDY
DBREF 1IDX A 1 9B PDB 1IDX 1IDX 1 9
SEQRES 1 A 18 DA DG DG DA DT DC DC DT DT DU DT DG DG
SEQRES 2 A 18 DA DT DC DC DT
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 - 23 20 Bytes