10 20 30 40 50 60 70 80 1CYZ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 31-AUG-99 1CYZ
TITLE NMR STRUCTURE OF THE GAACTGGTTC/TRI-IMIDAZOLE POLYAMIDE TITLE 2 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
EXPDTA SOLUTION NMR
AUTHOR X.-L.YANG,R.B.HUBBARD IV,M.LEE,Z.-F.TAO,H.SUGIYAMA,A.H.- AUTHOR 2 J.WANG
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 JRNL TITL 2 RECOGNITION MOTIF 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 REMARK 1 TITL 2 GROOVE BINDER, TO CCGG SEQUENCE ANALYZED BY NMR REMARK 1 TITL 3 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 : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1CYZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-99. REMARK 100 THE RCSB ID CODE IS RCSB009629.
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 REMARK 210 90% 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 : FELIX 1.1 AND 98 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 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. = 4.6 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 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-1H-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