Header list of 1g5d.pdb file
Complete list - 23 20 Bytes
HEADER DNA 31-OCT-00 1G5D
TITLE NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA
TITLE 2 ANOMER
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*TP*GP*GP*G)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3';
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DAMAGED DNA, APYRIMIDINIC SITE, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR S.T.HOEHN,C.J.TURNER,J.STUBBE
REVDAT 3 23-FEB-22 1G5D 1 REMARK LINK
REVDAT 2 24-FEB-09 1G5D 1 VERSN
REVDAT 1 22-AUG-01 1G5D 0
JRNL AUTH S.T.HOEHN,C.J.TURNER,J.STUBBE
JRNL TITL SOLUTION STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN
JRNL TITL 2 ABASIC SITE: EVIDENCE FOR AN UNUSUAL DEOXYRIBOSE
JRNL TITL 3 CONFORMATION.
JRNL REF NUCLEIC ACIDS RES. V. 29 3413 2001
JRNL REFN ISSN 0305-1048
JRNL PMID 11504879
JRNL DOI 10.1093/NAR/29.16.3413
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851, X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 475 NOE
REMARK 3 -DERIVED DISTANCE CONSTRAINTS AND 101 DIHEDRAL ANGLE RESTRAINTS.
REMARK 4
REMARK 4 1G5D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-00.
REMARK 100 THE DEPOSITION ID IS D_1000012253.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293; 278; 298
REMARK 210 PH : 6.8; 6.8; 6.8
REMARK 210 IONIC STRENGTH : 10 MM SODIUM PHOSPHATE BUFFER;
REMARK 210 10 MM SODIUM PHOSPHATE BUFFER;
REMARK 210 10 MM SODIUM PHOSPHATE BUFFER
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 2.5 MM ABASIC SITE CONTAINING
REMARK 210 DUPLEX OLIGONUCLEOTIDE; 10 MM
REMARK 210 SODIUM PHOSPHATE BUFFER; 2.5 MM
REMARK 210 ABASIC SITE CONTAINING DUPLEX
REMARK 210 OLIGONUCLEOTIDE; 10 MM SODIUM
REMARK 210 PHOSPHATE BUFFER; 3 MM ABASIC
REMARK 210 SITE CONTAINING DUPLEX
REMARK 210 OLIGONUCLEOTIDE; 10 MM SODIUM
REMARK 210 PHOSPHATE BUFFER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; PE-COSY; WATERGATE-NOESY;
REMARK 210 31P-HCOSY; 31P-DECOUPLED-PE-COSY;
REMARK 210 31P-DECOUPLED-J-SCALED-DQCOSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : HOME-BUILT
REMARK 210 SPECTROMETER MANUFACTURER : HOME-BUILT
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 95.0
REMARK 210 METHOD USED : MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 10
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE ABASIC SITE DEOXYRIBOSE 1H-1H COUPLING CONSTANTS AND
REMARK 210 THE DNA 31P-H3' COUPLING CONSTANTS WERE EXPERIMENTALLY
REMARK 210 DETERMINED. THIS INFORMATION WAS USED IN THE MODELING PROTOCOL.
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 DA A 4 N9 DA A 4 C4 0.037
REMARK 500 1 DT A 10 C5' DT A 10 C4' 0.044
REMARK 500 1 DG B 25 C8 DG B 25 N9 -0.043
REMARK 500 2 DA A 4 N9 DA A 4 C4 0.036
REMARK 500 2 DT A 10 C5' DT A 10 C4' 0.043
REMARK 500 2 DT B 24 C5' DT B 24 C4' 0.043
REMARK 500 3 DA A 4 N9 DA A 4 C4 0.037
REMARK 500 4 DA A 4 N9 DA A 4 C4 0.036
REMARK 500 4 DT A 10 C5' DT A 10 C4' 0.043
REMARK 500 4 DC B 16 C5' DC B 16 C4' 0.042
REMARK 500 4 DT B 24 C5' DT B 24 C4' 0.043
REMARK 500 5 DA A 4 N9 DA A 4 C4 0.036
REMARK 500 5 DC B 16 C5' DC B 16 C4' 0.042
REMARK 500 5 DA B 17 C5' DA B 17 C4' 0.042
REMARK 500 6 DT B 24 C5' DT B 24 C4' 0.043
REMARK 500 7 DT B 24 C5' DT B 24 C4' 0.043
REMARK 500 8 DA A 4 N9 DA A 4 C4 0.036
REMARK 500 8 DT A 10 C5' DT A 10 C4' 0.043
REMARK 500 9 DT A 10 C5' DT A 10 C4' 0.043
REMARK 500 9 DA B 20 C5' DA B 20 C4' 0.043
REMARK 500 9 DT B 24 C5' DT B 24 C4' 0.043
REMARK 500 10 DA A 4 N9 DA A 4 C4 0.038
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 3 N1 - C6 - N6 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = 5.5 DEGREES
REMARK 500 1 DA A 5 C5 - C6 - N6 ANGL. DEV. = -4.9 DEGREES
REMARK 500 1 DG A 6 N3 - C2 - N2 ANGL. DEV. = 5.4 DEGREES
REMARK 500 1 DA A 8 N1 - C6 - N6 ANGL. DEV. = 5.3 DEGREES
REMARK 500 1 DA A 8 C5 - C6 - N6 ANGL. DEV. = -5.1 DEGREES
REMARK 500 1 DG A 12 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 DG A 13 N3 - C2 - N2 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 DA B 17 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 DA B 17 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES
REMARK 500 1 DG B 18 N3 - C2 - N2 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 DA B 20 N1 - C6 - N6 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 DC B 21 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES
REMARK 500 1 DG B 25 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DG B 26 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = 5.1 DEGREES
REMARK 500 2 DG A 6 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 DA A 8 N1 - C6 - N6 ANGL. DEV. = 4.9 DEGREES
REMARK 500 2 DG A 12 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 DG A 13 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES
REMARK 500 2 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 2 DA B 17 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 DA B 17 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES
REMARK 500 2 DG B 18 N3 - C2 - N2 ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 DC B 21 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES
REMARK 500 2 DG B 26 N3 - C2 - N2 ANGL. DEV. = 4.7 DEGREES
REMARK 500 3 DA A 3 N1 - C6 - N6 ANGL. DEV. = 3.9 DEGREES
REMARK 500 3 DA A 5 N1 - C6 - N6 ANGL. DEV. = 4.9 DEGREES
REMARK 500 3 DG A 6 N3 - C2 - N2 ANGL. DEV. = 5.4 DEGREES
REMARK 500 3 DA A 8 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES
REMARK 500 3 DG A 12 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 DG A 13 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES
REMARK 500 3 DC B 14 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 3 DA B 17 N1 - C6 - N6 ANGL. DEV. = 3.9 DEGREES
REMARK 500 3 DG B 18 N3 - C2 - N2 ANGL. DEV. = 4.4 DEGREES
REMARK 500 3 DA B 20 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES
REMARK 500 3 DC B 21 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES
REMARK 500 3 DG B 26 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES
REMARK 500 4 DA A 3 N1 - C6 - N6 ANGL. DEV. = 4.0 DEGREES
REMARK 500 4 DA A 5 N1 - C6 - N6 ANGL. DEV. = 5.1 DEGREES
REMARK 500 4 DG A 6 N3 - C2 - N2 ANGL. DEV. = 5.2 DEGREES
REMARK 500 4 DA A 8 N1 - C6 - N6 ANGL. DEV. = 5.2 DEGREES
REMARK 500 4 DG A 12 N3 - C2 - N2 ANGL. DEV. = 5.0 DEGREES
REMARK 500 4 DG A 13 N3 - C2 - N2 ANGL. DEV. = 5.9 DEGREES
REMARK 500 4 DC B 14 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 4 DA B 17 N1 - C6 - N6 ANGL. DEV. = 4.8 DEGREES
REMARK 500 4 DG B 18 N3 - C2 - N2 ANGL. DEV. = 4.9 DEGREES
REMARK 500 4 DA B 20 N1 - C6 - N6 ANGL. DEV. = 3.9 DEGREES
REMARK 500 4 DC B 21 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 124 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 DA A 8 0.08 SIDE CHAIN
REMARK 500 1 DC A 9 0.07 SIDE CHAIN
REMARK 500 1 DG A 11 0.07 SIDE CHAIN
REMARK 500 1 DA B 20 0.06 SIDE CHAIN
REMARK 500 1 DT B 22 0.06 SIDE CHAIN
REMARK 500 1 DT B 23 0.06 SIDE CHAIN
REMARK 500 1 DG B 25 0.06 SIDE CHAIN
REMARK 500 2 DG A 6 0.08 SIDE CHAIN
REMARK 500 2 DA A 8 0.10 SIDE CHAIN
REMARK 500 2 DT A 10 0.07 SIDE CHAIN
REMARK 500 2 DG A 11 0.09 SIDE CHAIN
REMARK 500 2 DC B 16 0.07 SIDE CHAIN
REMARK 500 2 DA B 20 0.06 SIDE CHAIN
REMARK 500 2 DG B 25 0.08 SIDE CHAIN
REMARK 500 3 DG A 6 0.09 SIDE CHAIN
REMARK 500 3 DA A 8 0.10 SIDE CHAIN
REMARK 500 3 DG A 11 0.09 SIDE CHAIN
REMARK 500 3 DC B 16 0.07 SIDE CHAIN
REMARK 500 3 DG B 25 0.08 SIDE CHAIN
REMARK 500 4 DG A 6 0.09 SIDE CHAIN
REMARK 500 4 DA A 8 0.08 SIDE CHAIN
REMARK 500 4 DC A 9 0.08 SIDE CHAIN
REMARK 500 4 DG A 11 0.08 SIDE CHAIN
REMARK 500 4 DG B 25 0.08 SIDE CHAIN
REMARK 500 5 DG A 6 0.08 SIDE CHAIN
REMARK 500 5 DG A 11 0.09 SIDE CHAIN
REMARK 500 5 DG B 25 0.08 SIDE CHAIN
REMARK 500 6 DG A 6 0.09 SIDE CHAIN
REMARK 500 6 DA A 8 0.10 SIDE CHAIN
REMARK 500 6 DC A 9 0.08 SIDE CHAIN
REMARK 500 6 DG A 11 0.07 SIDE CHAIN
REMARK 500 6 DA B 20 0.06 SIDE CHAIN
REMARK 500 6 DG B 25 0.09 SIDE CHAIN
REMARK 500 7 DG A 6 0.09 SIDE CHAIN
REMARK 500 7 DA A 8 0.10 SIDE CHAIN
REMARK 500 7 DG A 11 0.09 SIDE CHAIN
REMARK 500 7 DC B 16 0.07 SIDE CHAIN
REMARK 500 7 DG B 25 0.08 SIDE CHAIN
REMARK 500 8 DG A 6 0.09 SIDE CHAIN
REMARK 500 8 DA A 8 0.10 SIDE CHAIN
REMARK 500 8 DC A 9 0.08 SIDE CHAIN
REMARK 500 8 DG A 11 0.07 SIDE CHAIN
REMARK 500 8 DG A 13 0.06 SIDE CHAIN
REMARK 500 8 DA B 20 0.06 SIDE CHAIN
REMARK 500 8 DG B 25 0.09 SIDE CHAIN
REMARK 500 9 DG A 6 0.08 SIDE CHAIN
REMARK 500 9 DA A 8 0.09 SIDE CHAIN
REMARK 500 9 DT A 10 0.07 SIDE CHAIN
REMARK 500 9 DG A 11 0.09 SIDE CHAIN
REMARK 500 9 DC B 16 0.08 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 56 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1A9I RELATED DB: PDB
REMARK 900 APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, ALPHA FORM,
REMARK 900 NMR, 1 STRUCTURE
REMARK 900 RELATED ID: 1A9J RELATED DB: PDB
REMARK 900 APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, BETA FORM,
REMARK 900 NMR, 1 STRUCTURE
REMARK 900 RELATED ID: 1GIZ RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE: NMR STRUCTURE OF AN OLIGONUCLEOTIDE
REMARK 900 CONTAINING AN ABASIC SITE: ALPHA ANOMER
REMARK 900 RELATED ID: 1G5E RELATED DB: PDB
REMARK 900 ENSEMBLE: NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC
REMARK 900 SITE: BETA ANOMER
REMARK 900 RELATED ID: 1GJ0 RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE: NMR STRUCTURE OF AN OLIGONUCLEOTIDE
REMARK 900 CONTAINING AN ABASIC SITE: BETA ANOMER
DBREF 1G5D A 1 13 PDB 1G5D 1G5D 1 13
DBREF 1G5D B 14 26 PDB 1G5D 1G5D 14 26
SEQRES 1 A 13 DC DC DA DA DA DG ORP DA DC DT DG DG DG
SEQRES 1 B 13 DC DC DC DA DG DT DA DC DT DT DT DG DG
HET ORP A 7 20
HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE
FORMUL 1 ORP C5 H11 O7 P
LINK O3' DG A 6 P ORP A 7 1555 1555 1.58
LINK O3 ORP A 7 P DA A 8 1555 1555 1.59
CRYST1 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