Header list of 1gn7.pdb file
Complete list - 23 20 Bytes
HEADER DNA 22-NOV-96 1GN7 TITLE NMR STRUCTURE OF AN INTRAMOLECULAR DNA TRIPLEX CONTAINING AN N7- TITLE 2 GLYCOSYLATED GUANINE, 8 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D COMPND 3 (*AP*GP*AP*GP*AP*GP*AP*AP*CP*CP*CP*CP*TP*TP*CP*TP*CP*TP* COMPND 4 CP*TP*TP*AP*TP*AP*TP*CP*TP*GN7*TP*CP*TP*T)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: THE GLYCOSYL LINK IN G28 IS TO ATOM N7, C26 AND C30 COMPND 8 ARE PROTONATED AT N3 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, TRIPLEX, N7-GUANINE, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR P.SCHULTZE,K.M.KOSHLAP,J.FEIGON REVDAT 3 23-FEB-22 1GN7 1 REMARK LINK REVDAT 2 24-FEB-09 1GN7 1 VERSN REVDAT 1 15-MAY-97 1GN7 0 JRNL AUTH K.M.KOSHLAP,P.SCHULTZE,H.BRUNAR,P.B.DERVAN,J.FEIGON JRNL TITL SOLUTION STRUCTURE OF AN INTRAMOLECULAR DNA TRIPLEX JRNL TITL 2 CONTAINING AN N7-GLYCOSYLATED GUANINE WHICH MIMICS A JRNL TITL 3 PROTONATED CYTOSINE. JRNL REF BIOCHEMISTRY V. 36 2659 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9054573 JRNL DOI 10.1021/BI962438A REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.HUNZIKER,E.S.PRIESTLEY,H.BRUNAR,P.B.DERVAN REMARK 1 TITL DESIGN OF AN N-7-GLYCOSYLATED PURINE NUCLEOSIDE FOR REMARK 1 TITL 2 RECOGNITION OF GC BASE PAIRS BY TRIPLE HELIX FORMATION REMARK 1 REF J.AM.CHEM.SOC. V. 117 2661 1995 REMARK 1 REFN ISSN 0002-7863 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: NULL REMARK 4 REMARK 4 1GN7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173626. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; HOENOE; HOHAHA; P.COSY; H REMARK 210 -C HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : GN500; AMX500; DRX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : BEST OVERALL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 H2'' DA A 8 O4' DC A 9 1.45 REMARK 500 H61 DA A 5 O4 DT A 16 1.58 REMARK 500 H62 DA A 5 O4 DT A 29 1.59 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 1 DG A 2 C5' DG A 2 C4' 0.045 REMARK 500 1 DG A 2 C3' DG A 2 C2' 0.099 REMARK 500 1 DG A 2 C2' DG A 2 C1' 0.068 REMARK 500 1 DG A 2 O4' DG A 2 C1' 0.095 REMARK 500 1 DG A 2 O4' DG A 2 C4' 0.090 REMARK 500 1 DG A 2 C1' DG A 2 N9 0.139 REMARK 500 1 DG A 2 C8 DG A 2 N9 0.059 REMARK 500 1 DG A 2 N9 DG A 2 C4 0.083 REMARK 500 1 DA A 3 C5' DA A 3 C4' 0.141 REMARK 500 1 DA A 3 C4' DA A 3 C3' 0.130 REMARK 500 1 DA A 3 C2' DA A 3 C1' 0.212 REMARK 500 1 DA A 3 C8 DA A 3 N9 -0.063 REMARK 500 1 DG A 4 C3' DG A 4 C2' 0.077 REMARK 500 1 DG A 4 C2' DG A 4 C1' 0.089 REMARK 500 1 DG A 4 C1' DG A 4 N9 0.081 REMARK 500 1 DG A 4 C2 DG A 4 N3 0.064 REMARK 500 1 DG A 4 N9 DG A 4 C4 0.098 REMARK 500 1 DA A 5 C5' DA A 5 C4' 0.089 REMARK 500 1 DA A 5 C4' DA A 5 C3' 0.076 REMARK 500 1 DA A 5 C5 DA A 5 N7 0.039 REMARK 500 1 DA A 5 N9 DA A 5 C4 0.044 REMARK 500 1 DG A 6 C5' DG A 6 C4' 0.047 REMARK 500 1 DG A 6 O4' DG A 6 C1' 0.074 REMARK 500 1 DG A 6 C8 DG A 6 N9 -0.044 REMARK 500 1 DG A 6 N9 DG A 6 C4 0.064 REMARK 500 1 DA A 7 C5' DA A 7 C4' 0.051 REMARK 500 1 DA A 7 C3' DA A 7 C2' 0.112 REMARK 500 1 DA A 7 C2' DA A 7 C1' 0.076 REMARK 500 1 DA A 8 C4' DA A 8 C3' 0.069 REMARK 500 1 DA A 8 C2' DA A 8 C1' 0.102 REMARK 500 1 DA A 8 N9 DA A 8 C4 0.051 REMARK 500 1 DC A 9 C2' DC A 9 C1' 0.071 REMARK 500 1 DC A 9 C5 DC A 9 C6 0.052 REMARK 500 1 DC A 10 C5' DC A 10 C4' 0.082 REMARK 500 1 DC A 10 C2' DC A 10 C1' 0.113 REMARK 500 1 DC A 10 N1 DC A 10 C6 0.043 REMARK 500 1 DC A 10 O3' DC A 11 P 0.092 REMARK 500 1 DC A 11 C5' DC A 11 C4' 0.076 REMARK 500 1 DC A 11 C4' DC A 11 C3' 0.089 REMARK 500 1 DC A 11 O3' DC A 12 P 0.116 REMARK 500 1 DC A 12 P DC A 12 O5' 0.105 REMARK 500 1 DC A 12 C5' DC A 12 C4' 0.138 REMARK 500 1 DC A 12 C4' DC A 12 C3' 0.062 REMARK 500 1 DC A 12 C3' DC A 12 C2' 0.125 REMARK 500 1 DC A 12 C2' DC A 12 C1' 0.130 REMARK 500 1 DT A 13 N1 DT A 13 C2 0.062 REMARK 500 1 DT A 13 C5 DT A 13 C7 0.042 REMARK 500 1 DT A 14 C5 DT A 14 C7 0.053 REMARK 500 1 DT A 16 C5' DT A 16 C4' 0.042 REMARK 500 1 DT A 16 C2 DT A 16 N3 0.049 REMARK 500 REMARK 500 THIS ENTRY HAS 817 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 DA A 1 C4' - C3' - O3' ANGL. DEV. = -16.2 DEGREES REMARK 500 1 DA A 1 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 1 DG A 2 C5' - C4' - C3' ANGL. DEV. = -17.2 DEGREES REMARK 500 1 DG A 2 C5' - C4' - O4' ANGL. DEV. = 16.5 DEGREES REMARK 500 1 DG A 2 C1' - O4' - C4' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DG A 2 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 2 C3' - C2' - C1' ANGL. DEV. = 12.7 DEGREES REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -18.9 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 21.7 DEGREES REMARK 500 1 DG A 2 N3 - C4 - C5 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DG A 2 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 3 O3' - P - O5' ANGL. DEV. = -15.0 DEGREES REMARK 500 1 DA A 3 O5' - C5' - C4' ANGL. DEV. = -9.9 DEGREES REMARK 500 1 DA A 3 C1' - O4' - C4' ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DA A 3 N9 - C1' - C2' ANGL. DEV. = 14.5 DEGREES REMARK 500 1 DA A 3 C5 - N7 - C8 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 11.7 DEGREES REMARK 500 1 DA A 3 C8 - N9 - C4 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG A 4 O4' - C4' - C3' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DG A 4 C4' - C3' - C2' ANGL. DEV. = -15.8 DEGREES REMARK 500 1 DG A 4 C3' - C2' - C1' ANGL. DEV. = 20.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - C2' ANGL. DEV. = -19.9 DEGREES REMARK 500 1 DG A 4 N9 - C1' - C2' ANGL. DEV. = 11.2 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 4 N3 - C4 - C5 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 4 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 4 N3 - C4 - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DG A 4 N1 - C2 - N2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 4 N3 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DG A 4 N1 - C6 - O6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG A 4 C4 - N9 - C1' ANGL. DEV. = 8.9 DEGREES REMARK 500 1 DG A 4 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 1 DA A 5 O4' - C4' - C3' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DA A 5 C1' - O4' - C4' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DA A 5 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 11.5 DEGREES REMARK 500 1 DA A 5 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 6 C5' - C4' - O4' ANGL. DEV. = 16.5 DEGREES REMARK 500 1 DG A 6 C4' - C3' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DG A 6 C3' - C2' - C1' ANGL. DEV. = 15.9 DEGREES REMARK 500 1 DG A 6 O4' - C1' - C2' ANGL. DEV. = -11.7 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DG A 6 N3 - C4 - C5 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 6 C4 - C5 - C6 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 6 C5 - N7 - C8 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1636 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 3 0.05 SIDE CHAIN REMARK 500 1 DC A 11 0.07 SIDE CHAIN REMARK 500 2 DC A 11 0.06 SIDE CHAIN REMARK 500 3 DC A 11 0.06 SIDE CHAIN REMARK 500 4 DA A 3 0.06 SIDE CHAIN REMARK 500 5 DC A 11 0.07 SIDE CHAIN REMARK 500 5 DT A 23 0.07 SIDE CHAIN REMARK 500 7 DC A 11 0.08 SIDE CHAIN REMARK 500 7 DT A 23 0.06 SIDE CHAIN REMARK 500 8 DA A 3 0.06 SIDE CHAIN REMARK 500 8 DC A 11 0.08 SIDE CHAIN REMARK 500 8 DT A 23 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1GN7 A 1 32 PDB 1GN7 1GN7 1 32 SEQRES 1 A 32 DA DG DA DG DA DG DA DA DC DC DC DC DT SEQRES 2 A 32 DT DC DT DC DT DC DT DT DA DT DA DT DC SEQRES 3 A 32 DT GN7 DT DC DT DT MODRES 1GN7 GN7 A 28 DG N7-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HET GN7 A 28 33 HETNAM GN7 N7-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 1 GN7 C10 H14 N5 O7 P LINK O3' DT A 27 P GN7 A 28 1555 1555 1.64 LINK O3' GN7 A 28 P DT A 29 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 - 23 20 Bytes