Header list of 1ycw.pdb file
Complete list - 25 20 Bytes
HEADER DNA 23-DEC-04 1YCW TITLE CLUSTERED ABASIC LESIONS IN DNA: NMR SOLUTION STRUCTURES 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*CP*CP*(3DR)P*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 1YCW 1 JRNL REVDAT 2 24-FEB-09 1YCW 1 VERSN REVDAT 1 06-DEC-05 1YCW 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 1YCW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-DEC-04. REMARK 100 THE RCSB ID CODE IS RCSB031386. 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, 25MM PHOSPHATE REMARK 210 BUFFER, 50MM NACL, 0.5MM 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 0.099 REMARK 500 1 DG A 2 C2 DG A 2 N2 0.086 REMARK 500 1 DC A 3 C4 DC A 3 N4 0.096 REMARK 500 1 DA A 4 C6 DA A 4 N6 0.095 REMARK 500 1 DT A 5 C5 DT A 5 C7 0.039 REMARK 500 1 DG A 6 C2 DG A 6 N2 0.089 REMARK 500 1 DG A 8 C2 DG A 8 N2 0.083 REMARK 500 1 DA A 10 C6 DA A 10 N6 0.097 REMARK 500 1 DC A 11 C4 DC A 11 N4 0.096 REMARK 500 1 DG A 12 C2 DG A 12 N2 0.084 REMARK 500 1 DC A 13 C4 DC A 13 N4 0.095 REMARK 500 1 DG B 14 C2 DG B 14 N2 0.086 REMARK 500 1 DC B 15 C4 DC B 15 N4 0.095 REMARK 500 1 DG B 16 C2 DG B 16 N2 0.083 REMARK 500 1 DT B 17 C5 DT B 17 C7 0.039 REMARK 500 1 DA B 18 C6 DA B 18 N6 0.094 REMARK 500 1 DC B 19 C4 DC B 19 N4 0.095 REMARK 500 1 DC B 20 C4 DC B 20 N4 0.096 REMARK 500 1 DA B 22 C6 DA B 22 N6 0.096 REMARK 500 1 DG B 24 C2 DG B 24 N2 0.086 REMARK 500 1 DC B 25 C4 DC B 25 N4 0.094 REMARK 500 1 DG B 26 C2 DG B 26 N2 0.089 REMARK 500 2 DC A 1 C4 DC A 1 N4 0.096 REMARK 500 2 DG A 2 C2 DG A 2 N2 0.085 REMARK 500 2 DC A 3 C4 DC A 3 N4 0.095 REMARK 500 2 DA A 4 C6 DA A 4 N6 0.094 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.038 REMARK 500 2 DG A 6 C2 DG A 6 N2 0.088 REMARK 500 2 DG A 8 C2 DG A 8 N2 0.083 REMARK 500 2 DA A 10 C6 DA A 10 N6 0.097 REMARK 500 2 DC A 11 C4 DC A 11 N4 0.096 REMARK 500 2 DG A 12 C2 DG A 12 N2 0.084 REMARK 500 2 DC A 13 C4 DC A 13 N4 0.095 REMARK 500 2 DG B 14 C2 DG B 14 N2 0.086 REMARK 500 2 DC B 15 C4 DC B 15 N4 0.097 REMARK 500 2 DG B 16 C2 DG B 16 N2 0.083 REMARK 500 2 DT B 17 C5 DT B 17 C7 0.038 REMARK 500 2 DA B 18 C6 DA B 18 N6 0.093 REMARK 500 2 DC B 19 C4 DC B 19 N4 0.093 REMARK 500 2 DC B 20 C4 DC B 20 N4 0.095 REMARK 500 2 DA B 22 C6 DA B 22 N6 0.097 REMARK 500 2 DG B 24 C2 DG B 24 N2 0.085 REMARK 500 2 DC B 25 C4 DC B 25 N4 0.095 REMARK 500 2 DG B 26 C2 DG B 26 N2 0.090 REMARK 500 3 DC A 1 C4 DC A 1 N4 0.097 REMARK 500 3 DG A 2 C2 DG A 2 N2 0.086 REMARK 500 3 DC A 3 C4 DC A 3 N4 0.095 REMARK 500 3 DA A 4 C6 DA A 4 N6 0.094 REMARK 500 3 DT A 5 C5 DT A 5 C7 0.038 REMARK 500 3 DG A 6 C2 DG A 6 N2 0.089 REMARK 500 REMARK 500 THIS ENTRY HAS 113 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 8 C1' - O4' - C4' ANGL. DEV. = -9.2 DEGREES REMARK 500 1 DT A 9 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DT A 9 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 8 C3' - O3' - P ANGL. DEV. = 11.1 DEGREES REMARK 500 1 DA A 10 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 23.8 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 10 O3' - P - O5' ANGL. DEV. = -11.8 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 13 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG B 16 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA B 18 C5' - C4' - O4' ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DA B 18 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC B 19 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG B 24 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG B 26 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG B 26 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 2 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 8 C1' - O4' - C4' ANGL. DEV. = -9.1 DEGREES REMARK 500 2 DT A 9 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 2 DT A 9 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DG A 8 C3' - O3' - P ANGL. DEV. = 11.4 DEGREES REMARK 500 2 DA A 10 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DA A 10 O4' - C1' - N9 ANGL. DEV. = 24.2 DEGREES REMARK 500 2 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DA A 10 O3' - P - O5' ANGL. DEV. = -11.5 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG B 16 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA B 18 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES REMARK 500 2 DA B 18 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DC B 20 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DA B 22 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 129 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 40.0 D L WRONG HAND REMARK 500 1 3DR B 21 41.8 D L WRONG HAND REMARK 500 2 3DR A 7 40.4 D L WRONG HAND REMARK 500 2 3DR B 21 41.8 D L WRONG HAND REMARK 500 5 3DR A 7 40.5 D L WRONG HAND REMARK 500 5 3DR B 21 42.0 D L WRONG HAND REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YCT RELATED DB: PDB REMARK 900 CLUSTERED ABASIC LESIONS IN DNA: NMR SOLUTION STRUCTURE OF REMARK 900 CLUSTERED BISTRANDED +1 ABASIC LESION REMARK 900 RELATED ID: 1HT4 RELATED DB: PDB REMARK 900 STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE REMARK 900 LESION STAGGERED IN A 3'-ORIENTATION 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 1YCW A 1 13 PDB 1YCW 1YCW 1 13 DBREF 1YCW B 14 26 PDB 1YCW 1YCW 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 DC DC 3DR 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 1.62 LINK O3' 3DR A 7 P DG A 8 1555 1555 1.62 LINK O3' DC B 20 P 3DR B 21 1555 1555 1.61 LINK O3' 3DR B 21 P DA B 22 1555 1555 1.61 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