Header list of 1yct.pdb file
Complete list - 25 20 Bytes
HEADER DNA 23-DEC-04 1YCT
TITLE CLUSTERED ABASIC LESIONS IN DNA: NMR SOLUTION STRUCTURE OF CLUSTERED
TITLE 2 BISTRANDED +1 ABASIC LESION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*AP*TP*GP*(3DR)P*GP*TP*AP*CP*GP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(3DR)P*CP*CP*AP*TP*GP*CP*G)-3';
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: RANDOMLY DESIGNED SEQUENCE CONTAINING STABLE ABASIC
SOURCE 4 SITES (3DR);
SOURCE 5 MOL_ID: 2;
SOURCE 6 SYNTHETIC: YES;
SOURCE 7 OTHER_DETAILS: RANDOMLY DESIGNED SEQUENCE CONTAINING STABLE ABASIC
SOURCE 8 SITES (3DR)
KEYWDS DOUBLE HELIX, ABASIC SITES, CLUSTERED DAMAGE, EXTRUDED RESIDUES,
KEYWDS 2 REDUCED AP SITE, FURAN, BISTRANDED ABASIC LESION., DNA
EXPDTA SOLUTION NMR
NUMMDL 5
AUTHOR R.D.HAZEL,C.DE LOS SANTOS
REVDAT 3 08-SEP-10 1YCT 1 JRNL
REVDAT 2 24-FEB-09 1YCT 1 VERSN
REVDAT 1 10-JAN-06 1YCT 0
JRNL AUTH R.D.HAZEL,K.TIAN,C.DE LOS SANTOS
JRNL TITL NMR SOLUTION STRUCTURES OF BISTRANDED ABASIC SITE LESIONS IN
JRNL TITL 2 DNA.
JRNL REF BIOCHEMISTRY V. 47 11909 2008
JRNL REFN ISSN 0006-2960
JRNL PMID 18950195
JRNL DOI 10.1021/BI800950T
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : A. BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: 1) HEATING STAGE: FROM 150 TO 500 K IN
REMARK 3 70PS. INTRODUCTION OF EXPERIMENTAL RESTRAINTS AT THE END OF THIS
REMARK 3 STAGE. 2) HIGH TEMPERATURE STAGE: 50 PS DYNAMICS AT 500K 3)
REMARK 3 COOLING STAGE: FROM 500 TO 300K IN 40PS. 4) EQUILIBRATION STAGE:
REMARK 3 120PS DYNAMICS AT 300K
REMARK 4
REMARK 4 1YCT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-04.
REMARK 100 THE RCSB ID CODE IS RCSB031383.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : NOT DETERMINED
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 2MM DUPLEX, 25 MM PHOSPHATE
REMARK 210 BUFFER, 50 MM NACL, 0.5 MM EDTA.
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY;
REMARK 210 COSY, COSY45
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, INSIGHT 95, MIDAS
REMARK 210 PLUS, CURVES 5
REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR 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: 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 0.085
REMARK 500 1 DC A 3 C4 DC A 3 N4 0.095
REMARK 500 1 DA A 4 C6 DA A 4 N6 0.096
REMARK 500 1 DG A 6 C2 DG A 6 N2 0.089
REMARK 500 1 DG A 8 C2 DG A 8 N2 0.088
REMARK 500 1 DT A 9 C5 DT A 9 C7 0.037
REMARK 500 1 DA A 10 C6 DA A 10 N6 0.096
REMARK 500 1 DC A 11 C4 DC A 11 N4 0.095
REMARK 500 1 DG A 12 C2 DG A 12 N2 0.086
REMARK 500 1 DC A 13 C4 DC A 13 N4 0.096
REMARK 500 1 DG B 14 C2 DG B 14 N2 0.087
REMARK 500 1 DC B 15 C4 DC B 15 N4 0.096
REMARK 500 1 DG B 16 C2 DG B 16 N2 0.087
REMARK 500 1 DT B 17 C5 DT B 17 C7 0.038
REMARK 500 1 DA B 18 C6 DA B 18 N6 0.096
REMARK 500 1 DC B 20 C4 DC B 20 N4 0.096
REMARK 500 1 DC B 19 C4 DC B 19 N4 0.095
REMARK 500 1 DA B 22 C6 DA B 22 N6 0.096
REMARK 500 1 DT B 23 C5 DT B 23 C7 0.037
REMARK 500 1 DG B 24 C2 DG B 24 N2 0.087
REMARK 500 1 DC B 25 C4 DC B 25 N4 0.096
REMARK 500 1 DG B 26 C2 DG B 26 N2 0.089
REMARK 500 2 DC A 1 C4 DC A 1 N4 0.097
REMARK 500 2 DG A 2 C2 DG A 2 N2 0.086
REMARK 500 2 DC A 3 C4 DC A 3 N4 0.096
REMARK 500 2 DA A 4 C6 DA A 4 N6 0.093
REMARK 500 2 DG A 6 C2 DG A 6 N2 0.089
REMARK 500 2 DG A 8 C2 DG A 8 N2 0.090
REMARK 500 2 DT A 9 C5 DT A 9 C7 0.038
REMARK 500 2 DA A 10 C6 DA A 10 N6 0.095
REMARK 500 2 DC A 11 C4 DC A 11 N4 0.097
REMARK 500 2 DG A 12 C2 DG A 12 N2 0.085
REMARK 500 2 DC A 13 C4 DC A 13 N4 0.096
REMARK 500 2 DG B 14 C2 DG B 14 N2 0.087
REMARK 500 2 DC B 15 C4 DC B 15 N4 0.097
REMARK 500 2 DG B 16 C2 DG B 16 N2 0.086
REMARK 500 2 DT B 17 C5 DT B 17 C7 0.037
REMARK 500 2 DA B 18 C6 DA B 18 N6 0.096
REMARK 500 2 DC B 20 C4 DC B 20 N4 0.094
REMARK 500 2 DC B 19 C4 DC B 19 N4 0.092
REMARK 500 2 DA B 22 C6 DA B 22 N6 0.095
REMARK 500 2 DT B 23 C5 DT B 23 C7 0.036
REMARK 500 2 DG B 24 C2 DG B 24 N2 0.087
REMARK 500 2 DC B 25 C4 DC B 25 N4 0.096
REMARK 500 2 DG B 26 C2 DG B 26 N2 0.089
REMARK 500 3 DC A 1 C4 DC A 1 N4 0.097
REMARK 500 3 DG A 2 C2 DG A 2 N2 0.084
REMARK 500 3 DC A 3 C4 DC A 3 N4 0.093
REMARK 500 3 DA A 4 C6 DA A 4 N6 0.095
REMARK 500
REMARK 500 THIS ENTRY HAS 115 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 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES
REMARK 500 1 DG A 12 C5' - C4' - O4' ANGL. DEV. = 9.0 DEGREES
REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DG B 14 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 DG B 16 C5' - C4' - O4' ANGL. DEV. = 8.2 DEGREES
REMARK 500 1 DG B 16 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 1 DC B 20 O4' - C4' - C3' ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 DC B 20 C4' - C3' - C2' ANGL. DEV. = -7.2 DEGREES
REMARK 500 1 DC B 20 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES
REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DG B 24 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DC B 25 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 DG B 26 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 2 DG A 8 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 2 DG A 12 C5' - C4' - O4' ANGL. DEV. = 8.6 DEGREES
REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DG A 12 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 2 DG B 14 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 2 DG B 16 C5' - C4' - O4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 2 DG B 16 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DT B 17 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 2 DA B 18 C5' - C4' - O4' ANGL. DEV. = 8.2 DEGREES
REMARK 500 2 DC B 20 O4' - C4' - C3' ANGL. DEV. = 6.2 DEGREES
REMARK 500 2 DC B 20 C4' - C3' - C2' ANGL. DEV. = -7.3 DEGREES
REMARK 500 2 DC B 20 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES
REMARK 500 2 DC B 20 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 DG B 24 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DC B 25 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DG B 26 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 2 DG B 26 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 3 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 3 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 116 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 1 3DR A 7 41.7 D L WRONG HAND
REMARK 500 1 3DR B 21 41.7 D L WRONG HAND
REMARK 500 2 3DR A 7 41.9 D L WRONG HAND
REMARK 500 2 3DR B 21 41.8 D L WRONG HAND
REMARK 500 3 3DR A 7 42.1 D L WRONG HAND
REMARK 500 3 3DR B 21 41.8 D L WRONG HAND
REMARK 500 4 3DR A 7 41.8 D L WRONG HAND
REMARK 500 4 3DR B 21 41.8 D L WRONG HAND
REMARK 500 5 3DR A 7 41.8 D L WRONG HAND
REMARK 500 5 3DR B 21 41.8 D L WRONG HAND
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3DR A 7
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3DR B 21
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1HT7 RELATED DB: PDB
REMARK 900 STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE
REMARK 900 LESION STAGGERED IN A 5'-ORIENTATION
DBREF 1YCT A 1 13 PDB 1YCT 1YCT 1 13
DBREF 1YCT B 14 26 PDB 1YCT 1YCT 14 26
SEQRES 1 A 13 DC DG DC DA DT DG 3DR DG DT DA DC DG DC
SEQRES 1 B 13 DG DC DG DT DA 3DR DC DC DA DT DG DC DG
HET 3DR A 7 19
HET 3DR B 21 19
HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
HETSYN 3DR ABASIC DIDEOXYRIBOSE
FORMUL 1 3DR 2(C5 H11 O6 P)
LINK O3' DG A 6 P 3DR A 7 1555 1555 1.61
LINK O3' 3DR A 7 P DG A 8 1555 1555 1.62
LINK O3' DA B 18 P 3DR B 21 1555 1555 1.62
LINK P DC B 20 O3' 3DR B 21 1555 1555 1.61
SITE 1 AC1 2 DG A 6 DG A 8
SITE 1 AC2 3 DA B 18 DC B 19 DC B 20
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 - 25 20 Bytes