Header list of 1b6x.pdb file
Complete list - 25 20 Bytes
HEADER DNA 19-JAN-99 1B6X
TITLE 3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE GUANINE IN AN 11-MER DUPLEX,
TITLE 2 SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 4 STRUCTURES
CAVEAT 1B6X THERE IS A CHIRALITY ERROR AT ATOM C1' OF EDC A 6 IN MODEL
CAVEAT 2 1B6X 1.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*GP*TP*AP*CP*(EDC)P*CP*AP*TP*GP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*CP*AP*TP*GP*GP*GP*TP*AP*CP*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 DEOXYRIBONUCLEIC ACID, ETHENODC, EDC, EXOCYCLIC LESION, DNA
EXPDTA SOLUTION NMR
NUMMDL 4
AUTHOR D.CULLINAN,F.JOHNSON,A.P.GROLLMAN,M.EISENBERG,C.DE LOS SANTOS
REVDAT 5 18-JAN-12 1B6X 1 HETATM HETSYN FORMUL REMARK
REVDAT 4 24-FEB-09 1B6X 1 VERSN
REVDAT 3 01-APR-03 1B6X 1 JRNL
REVDAT 2 06-APR-99 1B6X 1 HET COMPND REMARK TITLE
REVDAT 2 2 1 HETATM SEQADV EXPDTA HEADER
REVDAT 2 3 1 MODRES LINK SOURCE AUTHOR
REVDAT 2 4 1 SEQRES FORMUL JRNL KEYWDS
REVDAT 2 5 1 HETSYN CONECT
REVDAT 1 27-JAN-99 1B6X 0
JRNL AUTH D.CULLINAN,F.JOHNSON,A.P.GROLLMAN,M.EISENBERG,
JRNL AUTH 2 C.DE LOS SANTOS
JRNL TITL SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING THE EXOCYCLIC
JRNL TITL 2 LESION 3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE
JRNL TITL 3 2'-DEOXYGUANOSINE.
JRNL REF BIOCHEMISTRY V. 36 11933 1997
JRNL REFN ISSN 0006-2960
JRNL PMID 9305987
JRNL DOI 10.1021/BI9705725
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE.
REMARK 4
REMARK 4 1B6X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
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 : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; DQF-COSY; TOCSY;
REMARK 210 COSY45; 15N-HMQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA; AM; AND AMX
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX, X-PLOR
REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS
REMARK 210 SIMULATIONS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 4
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D PROTON NMR FOLLOWED
REMARK 210 BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND
REMARK 210 FURTHER REFINED USING THE FULL RELAXATION MATRIX BACK CALCULATION
REMARK 210 APPROACH.
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 0.095
REMARK 500 1 DG A 2 C2 DG A 2 N2 0.081
REMARK 500 1 DT A 3 C5 DT A 3 C7 0.036
REMARK 500 1 DA A 4 C6 DA A 4 N6 0.094
REMARK 500 1 DC A 5 C4 DC A 5 N4 0.094
REMARK 500 1 DC A 7 C4 DC A 7 N4 0.096
REMARK 500 1 DA A 8 C6 DA A 8 N6 0.094
REMARK 500 1 DT A 9 C5 DT A 9 C7 0.036
REMARK 500 1 DG A 10 C2 DG A 10 N2 0.083
REMARK 500 1 DC A 11 C4 DC A 11 N4 0.097
REMARK 500 1 DG B 1 C2 DG B 1 N2 0.078
REMARK 500 1 DC B 2 C4 DC B 2 N4 0.093
REMARK 500 1 DA B 3 C6 DA B 3 N6 0.093
REMARK 500 1 DG B 5 C2 DG B 5 N2 0.080
REMARK 500 1 DG B 6 C2 DG B 6 N2 0.077
REMARK 500 1 DG B 7 C2 DG B 7 N2 0.084
REMARK 500 1 DT B 8 C5 DT B 8 C7 0.036
REMARK 500 1 DA B 9 C6 DA B 9 N6 0.095
REMARK 500 1 DC B 10 C4 DC B 10 N4 0.096
REMARK 500 1 DG B 11 C2 DG B 11 N2 0.084
REMARK 500 2 DC A 1 C4 DC A 1 N4 0.096
REMARK 500 2 DG A 2 C2 DG A 2 N2 0.080
REMARK 500 2 DA A 4 C6 DA A 4 N6 0.094
REMARK 500 2 DC A 5 C4 DC A 5 N4 0.096
REMARK 500 2 DC A 7 C4 DC A 7 N4 0.094
REMARK 500 2 DA A 8 C6 DA A 8 N6 0.094
REMARK 500 2 DG A 10 C2 DG A 10 N2 0.083
REMARK 500 2 DC A 11 C4 DC A 11 N4 0.096
REMARK 500 2 DG B 1 C2 DG B 1 N2 0.078
REMARK 500 2 DC B 2 C4 DC B 2 N4 0.093
REMARK 500 2 DA B 3 C6 DA B 3 N6 0.092
REMARK 500 2 DG B 5 C2 DG B 5 N2 0.082
REMARK 500 2 DG B 6 C2 DG B 6 N2 0.083
REMARK 500 2 DG B 7 C2 DG B 7 N2 0.083
REMARK 500 2 DT B 8 C5 DT B 8 C7 0.037
REMARK 500 2 DA B 9 C6 DA B 9 N6 0.095
REMARK 500 2 DC B 10 C4 DC B 10 N4 0.095
REMARK 500 2 DG B 11 C2 DG B 11 N2 0.084
REMARK 500 3 DC A 1 C4 DC A 1 N4 0.095
REMARK 500 3 DG A 2 C2 DG A 2 N2 0.081
REMARK 500 3 DA A 4 C6 DA A 4 N6 0.094
REMARK 500 3 DC A 5 C4 DC A 5 N4 0.094
REMARK 500 3 DC A 7 C4 DC A 7 N4 0.093
REMARK 500 3 DA A 8 C6 DA A 8 N6 0.094
REMARK 500 3 DG A 10 C2 DG A 10 N2 0.083
REMARK 500 3 DC A 11 C4 DC A 11 N4 0.096
REMARK 500 3 DG B 1 C2 DG B 1 N2 0.078
REMARK 500 3 DC B 2 C4 DC B 2 N4 0.094
REMARK 500 3 DA B 3 C6 DA B 3 N6 0.093
REMARK 500 3 DG B 5 C2 DG B 5 N2 0.082
REMARK 500
REMARK 500 THIS ENTRY HAS 75 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. = 2.1 DEGREES
REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES
REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DG B 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES
REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES
REMARK 500 2 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 2 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DG B 5 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 2 DG B 5 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DG B 6 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 3 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 3 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES
REMARK 500 3 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 3 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DG B 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 3 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 3 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 4 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 4 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 4 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 4 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 4 DC A 11 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES
REMARK 500 4 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 4 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 4 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 55 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 EDC A 6 28.1 D L WRONG HAND
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1B6X A 1 11 PDB 1B6X 1B6X 1 11
DBREF 1B6X B 1 11 PDB 1B6X 1B6X 1 11
SEQRES 1 A 11 DC DG DT DA DC EDC DC DA DT DG DC
SEQRES 1 B 11 DG DC DA DT DG DG DG DT DA DC DG
HET EDC A 6 32
HETNAM EDC N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
HETSYN EDC 6-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-
HETSYN 2 EDC PENTOFURANOSYL)IMIDAZO[1,2-C]PYRIMIDIN-5(6H)-ONE
FORMUL 1 EDC C11 H14 N3 O7 P
LINK P EDC A 6 O3' DC A 5 1555 1555 1.62
LINK O3' EDC A 6 P DC A 7 1555 1555 1.62
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