HEADER DNA 31-AUG-99 1CYZ TITLE NMR STRUCTURE OF THE GAACTGGTTC/TRI-IMIDAZOLE POLYAMIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*AP*AP*CP*TP*GP*GP*TP*TP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS T:G RECOGNIZED BY IM/IM PAIR IN THE DNA MINOR GROOVE, DNA EXPDTA SOLUTION NMR AUTHOR X.-L.YANG,R.B.HUBBARD IV,M.LEE,Z.-F.TAO,H.SUGIYAMA,A.H.-J.WANG REVDAT 5 22-MAY-24 1CYZ 1 REMARK REVDAT 4 16-FEB-22 1CYZ 1 COMPND REMARK HETNAM REVDAT 3 24-FEB-09 1CYZ 1 VERSN REVDAT 2 18-JAN-05 1CYZ 1 JRNL COMPND AUTHOR REMARK REVDAT 1 14-SEP-99 1CYZ 0 JRNL AUTH X.-L.YANG,R.B.HUBBARD IV,M.LEE,Z.-F.TAO,H.SUGIYAMA, JRNL AUTH 2 A.H.-J.WANG JRNL TITL IMIDAZOLE-IMIDAZOLE PAIR AS A MINOR GROOVE RECOGNITION MOTIF JRNL TITL 2 FOR T:G MISMATCHED BASE PAIRS JRNL REF NUCLEIC ACIDS RES. V. 27 4183 1999 JRNL REFN ISSN 0305-1048 JRNL PMID 10518609 JRNL DOI 10.1093/NAR/27.21.4183 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.-L.YANG,C.KAENZIG,M.LEE,A.H.-J.WANG REMARK 1 TITL BINDING OF AR-1-144, A TRI-IMIDAZOLE DNA MINOR GROOVE REMARK 1 TITL 2 BINDER, TO CCGG SEQUENCE ANALYZED BY NMR SPECTROSCOPY REMARK 1 REF EUR.J.BIOCHEM. V. 263 646 1999 REMARK 1 REFN ISSN 0014-2956 REMARK 1 DOI 10.1046/J.1432-1327.1999.00515.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 1.1 AND 98, X-PLOR 3.851 REMARK 3 AUTHORS : MSI (FELIX), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CYZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000009629. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 275 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NO ADDITIONAL SALT REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM DNA DUPLEX; 20 MM REMARK 210 PHOSPHATE BUFFER; 100% D2O OR 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NOE-RESTRAINED CONJUGATE REMARK 210 GRADIENT REFINEMENT IN X-PLOR; REMARK 210 FULL MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 11 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : REFINED AVERAGE STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR REMARK 210 TECHNIQUES WITH BACK NOE CALCULATION 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 DG A 1 C5' DG A 1 C4' 0.043 REMARK 500 DT A 5 C5 DT A 5 C7 0.044 REMARK 500 DG B 16 C5' DG B 16 C4' 0.044 REMARK 500 DT B 20 C5 DT B 20 C7 0.044 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 7 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 7 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 9.2 DEGREES REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG B 16 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA B 18 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 22 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 22 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT B 23 O4' - C1' - N1 ANGL. DEV. = 9.2 DEGREES REMARK 500 DT B 24 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES 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 AR1 A 12 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AR1 B 26 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B0S RELATED DB: PDB REMARK 900 1B0S CONTAINS THE NMR STRUCTURE OF GAACCGGTTC/TRI-IMIDAZOLE REMARK 900 POLYAMIDE COMPLEX DBREF 1CYZ A 1 10 PDB 1CYZ 1CYZ 1 10 DBREF 1CYZ B 16 25 PDB 1CYZ 1CYZ 16 25 SEQRES 1 A 10 DG DA DA DC DT DG DG DT DT DC SEQRES 1 B 10 DG DA DA DC DT DG DG DT DT DC HET AR1 A 12 63 HET AR1 B 26 63 HETNAM AR1 (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2- HETNAM 2 AR1 CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}- HETNAM 3 AR1 AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}- HETNAM 4 AR1 ETHYL)-DIMETHYL-AMMONIUM HETSYN AR1 TRI-IMIDAZOLE DNA MINOR GROOVE BINDER; AR-1-144 FORMUL 3 AR1 2(C20 H28 N11 O4 1+) SITE 1 AC1 10 DC A 4 DT A 5 DG A 6 DG A 7 SITE 2 AC1 10 DT A 8 DT A 9 DC B 19 DG B 21 SITE 3 AC1 10 DG B 22 AR1 B 26 SITE 1 AC2 10 DC A 4 DG A 6 DG A 7 AR1 A 12 SITE 2 AC2 10 DC B 19 DT B 20 DG B 21 DG B 22 SITE 3 AC2 10 DT B 23 DT B 24 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