Header list of 1fyi.pdb file
Complete list - 23 20 Bytes
HEADER DNA 30-SEP-00 1FYI
TITLE 11-MER DNA DUPLEX CONTAINING A 2'-DEOXYARISTEROMYCIN 8-OXO-GUANINE
TITLE 2 BASE PAIR;
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*AP*GP*TP*GP*(2AR)P*GP*TP*CP*AP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*TP*GP*AP*CP*(8OG)P*CP*AP*CP*TP*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 2'-DEOXYARISTEROMYCIN, 8-OXO-GUANINE, DNA
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR S.SMIRNOV,F.JOHNSON,C.DE LOS SANTOS
REVDAT 3 23-FEB-22 1FYI 1 REMARK LINK
REVDAT 2 24-FEB-09 1FYI 1 VERSN
REVDAT 1 18-OCT-00 1FYI 0
JRNL AUTH S.SMIRNOV,F.JOHNSON,C.DE LOS SANTOS
JRNL TITL STRUCTURAL NMR CHARACTERIZATION OF AN 11-MER DNA DUPLEX
JRNL TITL 2 CONTAINING A 2'-DEOXYARISTEROMYCIN 8-OXO-GUANINE PAIR,
JRNL TITL 3 NONHYDROLYZABLE SUBSTRATE ANALOG FOR THE DNA REPAIR ENZYME
JRNL TITL 4 MUTY
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 5, X-PLOR 3.8
REMARK 3 AUTHORS : VARIAN CO. (VNMR), A. BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1FYI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-OCT-00.
REMARK 100 THE DEPOSITION ID IS D_1000012016.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 284; 298
REMARK 210 PH : 6.8; 6.8
REMARK 210 IONIC STRENGTH : 50MM; 50MM
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 280 OD260 IN 0.6 ML OF 50 MM
REMARK 210 PHOSPHATE BUFFER, PH 6.8; 280
REMARK 210 OD260 IN 0.6 ML OF 50 MM
REMARK 210 PHOSPHATE BUFFER, PH 6.8
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 95
REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 15
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 4
REMARK 210
REMARK 210 REMARK: NULL
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 H41 DC A 11 H1 DG B 12 1.23
REMARK 500 N3 DC A 11 H21 DG B 12 1.28
REMARK 500 C2 DC A 11 H21 DG B 12 1.50
REMARK 500 O2 DC A 11 H21 DG B 12 1.56
REMARK 500 O2 DC A 11 N2 DG B 12 2.02
REMARK 500 N3 DC A 11 N2 DG B 12 2.17
REMARK 500
REMARK 500 REMARK: NULL
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 5 DT B 13 O3' DG B 14 P 0.136
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. = 3.2 DEGREES
REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES
REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES
REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DG B 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 DT B 13 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DG B 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DG B 14 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DA B 15 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DC B 16 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 DA B 19 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DA B 19 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DT B 21 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 2 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 2 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES
REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 2 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 2 DG B 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 302 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1EXL RELATED DB: PDB
REMARK 900 11-MER DNA DUPLEX CONTAINING THE CARBOCYCLIC NUCLEOTIDE ANALOG: 2'-
REMARK 900 DEOXYARISTEROMYCIN
DBREF 1FYI A 1 11 PDB 1FYI 1FYI 1 11
DBREF 1FYI B 12 22 PDB 1FYI 1FYI 12 22
SEQRES 1 A 11 DC DA DG DT DG 2AR DG DT DC DA DC
SEQRES 1 B 11 DG DT DG DA DC 8OG DC DA DC DT DG
MODRES 1FYI 2AR A 6 DA 2'-DEOXYARISTEROMYCIN-5'-PHOSPHATE
MODRES 1FYI 8OG B 17 DG
HET 2AR A 6 34
HET 8OG B 17 34
HETNAM 2AR 2'-DEOXYARISTEROMYCIN-5'-PHOSPHATE
HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETSYN 2AR [ADENIN-9-YL-3-HYDROXY-CYCLOPENTAN-5-YL]-METHYL-5'-
HETSYN 2 2AR PHOSPHATE
HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
FORMUL 1 2AR C11 H16 N5 O5 P
FORMUL 2 8OG C10 H14 N5 O8 P
LINK O3' DG A 5 P 2AR A 6 1555 1555 1.62
LINK O3' 2AR A 6 P DG A 7 1555 1555 1.62
LINK O3' DC B 16 P 8OG B 17 1555 1555 1.61
LINK O3' 8OG B 17 P DC B 18 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 - 23 20 Bytes