10 20 30 40 50 60 70 80 1P3X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 05-FEB-98 1P3X
TITLE INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN TITLE 2 THE THIRD STRAND, NMR, 10 STRUCTURES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A COMPND 6 8 AND T 9 AND BETWEEN T 16 AND T 17. C 18, C 20, AND C 22 COMPND 7 ARE PROTONATED; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*TP*TP*CP*TP*CP*TP*CP*T)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A COMPND 13 8 AND T 9 AND BETWEEN T 16 AND T 17. C 18, C 20, AND C 22 COMPND 14 ARE PROTONATED
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS OLIGONUCLEOTIDE, TRIPLEX, PROPYNE, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR A.K.PHIPPS,M.TARKOY,P.SCHULTZE,J.FEIGON
REVDAT 2 24-FEB-09 1P3X 1 VERSN REVDAT 1 06-MAY-98 1P3X 0
JRNL AUTH A.K.PHIPPS,M.TARKOY,P.SCHULTZE,J.FEIGON JRNL TITL SOLUTION STRUCTURE OF AN INTRAMOLECULAR DNA JRNL TITL 2 TRIPLEX CONTAINING 5-(1-PROPYNYL)-2'-DEOXYURIDINE JRNL TITL 3 RESIDUES IN THE THIRD STRAND. JRNL REF BIOCHEMISTRY V. 37 5820 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9558315 JRNL DOI 10.1021/BI972811U
REMARK 1
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: LAST REFINEMENT STEP USED RELAXATION REMARK 3 MATRIX REFINEMENT.
REMARK 4 REMARK 4 1P3X 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 : 5.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, DQF-COSY, TOCSY, HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX500, AMX500 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 : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST 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 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 DA A 1 C5' DA A 1 C4' 0.127 REMARK 500 1 DG A 2 C4' DG A 2 C3' 0.065 REMARK 500 1 DG A 2 C3' DG A 2 C2' 0.077 REMARK 500 1 DA A 3 C5' DA A 3 C4' 0.146 REMARK 500 1 DA A 3 C8 DA A 3 N9 -0.073 REMARK 500 1 DG A 6 C5' DG A 6 C4' 0.050 REMARK 500 1 DG A 6 C2' DG A 6 C1' 0.065 REMARK 500 1 DA A 8 C3' DA A 8 C2' -0.056 REMARK 500 1 DT B 10 C5 DT B 10 C7 0.037 REMARK 500 1 DT B 12 C5' DT B 12 C4' 0.042 REMARK 500 1 DT B 12 C3' DT B 12 C2' -0.069 REMARK 500 1 DC B 13 C5' DC B 13 C4' 0.052 REMARK 500 1 DT B 14 C5' DT B 14 C4' 0.049 REMARK 500 1 DT B 14 C3' DT B 14 C2' -0.077 REMARK 500 1 DT B 14 C5 DT B 14 C7 0.052 REMARK 500 1 DT B 16 C5' DT B 16 C4' 0.074 REMARK 500 2 DA A 1 C5' DA A 1 C4' 0.119 REMARK 500 2 DG A 2 C4' DG A 2 C3' 0.066 REMARK 500 2 DG A 2 C3' DG A 2 C2' 0.091 REMARK 500 2 DA A 3 C5' DA A 3 C4' 0.156 REMARK 500 2 DA A 3 C8 DA A 3 N9 -0.072 REMARK 500 2 DG A 6 C5' DG A 6 C4' 0.056 REMARK 500 2 DA A 8 C3' DA A 8 C2' -0.061 REMARK 500 2 DT B 12 C3' DT B 12 C2' -0.067 REMARK 500 2 DT B 12 C5 DT B 12 C7 0.044 REMARK 500 2 DC B 13 C5' DC B 13 C4' 0.053 REMARK 500 2 DC B 13 C3' DC B 13 C2' -0.051 REMARK 500 2 DT B 14 C5' DT B 14 C4' 0.065 REMARK 500 2 DT B 14 C3' DT B 14 C2' -0.085 REMARK 500 2 DT B 14 C5 DT B 14 C7 0.042 REMARK 500 2 DT B 16 C5' DT B 16 C4' 0.071 REMARK 500 2 DT B 16 C3' DT B 16 C2' -0.052 REMARK 500 3 DA A 1 C5' DA A 1 C4' 0.115 REMARK 500 3 DG A 2 C4' DG A 2 C3' 0.069 REMARK 500 3 DG A 2 C3' DG A 2 C2' 0.078 REMARK 500 3 DA A 3 C5' DA A 3 C4' 0.134 REMARK 500 3 DA A 3 C2' DA A 3 C1' 0.082 REMARK 500 3 DA A 3 C8 DA A 3 N9 -0.075 REMARK 500 3 DG A 6 C5' DG A 6 C4' 0.081 REMARK 500 3 DG A 6 C2' DG A 6 C1' 0.070 REMARK 500 3 DA A 8 C3' DA A 8 C2' -0.075 REMARK 500 3 DT B 10 C5' DT B 10 C4' 0.046 REMARK 500 3 DT B 12 C3' DT B 12 C2' -0.090 REMARK 500 3 DC B 13 C5 DC B 13 C6 0.057 REMARK 500 3 DT B 14 C5' DT B 14 C4' 0.049 REMARK 500 3 DT B 14 C4' DT B 14 C3' -0.091 REMARK 500 3 DC B 15 N1 DC B 15 C6 -0.037 REMARK 500 3 DT B 16 C3' DT B 16 C2' -0.065 REMARK 500 4 DA A 1 C5' DA A 1 C4' 0.112 REMARK 500 4 DG A 2 C4' DG A 2 C3' 0.065 REMARK 500 REMARK 500 THIS ENTRY HAS 165 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 O4' - C4' - C3' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DA A 1 C5' - C4' - C3' ANGL. DEV. = 12.9 DEGREES REMARK 500 1 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 1 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 3 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DA A 3 N9 - C1' - C2' ANGL. DEV. = 20.8 DEGREES REMARK 500 1 DA A 3 C5 - N7 - C8 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DA A 3 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DG A 4 O4' - C4' - C3' ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DG A 4 N9 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 1 DG A 4 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 5 N9 - C1' - C2' ANGL. DEV. = -11.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - C2' ANGL. DEV. = -9.2 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DA A 7 C5' - C4' - O4' ANGL. DEV. = 15.2 DEGREES REMARK 500 1 DA A 7 O4' - C1' - C2' ANGL. DEV. = -8.2 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 8 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 14.0 DEGREES REMARK 500 1 DT B 9 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT B 10 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT B 10 C3' - C2' - C1' ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT B 10 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT B 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC B 11 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT B 10 C3' - O3' - P ANGL. DEV. = 12.7 DEGREES REMARK 500 1 DC B 13 C5' - C4' - C3' ANGL. DEV. = 8.4 DEGREES REMARK 500 1 DC B 13 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DC B 13 C6 - N1 - C2 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 12 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 1 DT B 14 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DT B 14 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT B 14 C3' - C2' - C1' ANGL. DEV. = 12.2 DEGREES REMARK 500 1 DT B 14 O4' - C1' - C2' ANGL. DEV. = -11.9 DEGREES REMARK 500 1 DC B 13 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 1 DC B 15 O4' - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DC B 15 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DT B 14 C3' - O3' - P ANGL. DEV. = 17.3 DEGREES REMARK 500 1 DT B 16 C5' - C4' - O4' ANGL. DEV. = 16.1 DEGREES REMARK 500 1 DT B 16 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 578 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1 PDU A 17 REMARK 610 1 DCM A 20 REMARK 610 1 DC A 22 REMARK 610 2 PDU A 17 REMARK 610 2 DCM A 20 REMARK 610 2 DC A 22 REMARK 610 3 PDU A 17 REMARK 610 3 DCM A 20 REMARK 610 3 DC A 22 REMARK 610 4 PDU A 17 REMARK 610 4 DCM A 20 REMARK 610 4 DC A 22 REMARK 610 5 PDU A 17 REMARK 610 5 DCM A 20 REMARK 610 5 DC A 22 REMARK 610 6 PDU A 17 REMARK 610 6 DCM A 20 REMARK 610 6 DC A 22 REMARK 610 7 PDU A 17 REMARK 610 7 DCM A 20 REMARK 610 7 DC A 22 REMARK 610 8 PDU A 17 REMARK 610 8 DCM A 20 REMARK 610 8 DC A 22 REMARK 610 9 PDU A 17 REMARK 610 9 DCM A 20 REMARK 610 9 DC A 22 REMARK 610 10 PDU A 17 REMARK 610 10 DCM A 20 REMARK 610 10 DC A 22
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDU A 17 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DC A 18 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDU A 19 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCM A 20 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDU A 21 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DC A 22 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDU A 23 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDU A 24
DBREF 1P3X A 1 8 PDB 1P3X 1P3X 1 8 DBREF 1P3X B 9 16 PDB 1P3X 1P3X 9 16
SEQRES 1 A 8 DA DG DA DG DA DG DA DA SEQRES 1 B 8 DT DT DC DT DC DT DC DT
HET PDU A 17 31 HET DC A 18 31 HET PDU A 19 34 HET DCM A 20 31 HET PDU A 21 34 HET DC A 22 31 HET PDU A 23 34 HET PDU A 24 35
HETNAM PDU 5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE HETNAM DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
FORMUL 3 PDU 5(C12 H19 N2 O8 P) FORMUL 3 DC 2(C9 H14 N3 O7 P) FORMUL 3 DCM C9 H14 N3 O7 P
LINK O3' PDU A 17 P DC A 18 1555 1555 1.59 LINK O3' PDU A 19 P DCM A 20 1555 1555 1.61 LINK P PDU A 19 O3' DC A 18 1555 1555 1.65 LINK O3' PDU A 21 P DC A 22 1555 1555 1.61 LINK P PDU A 21 O3' DCM A 20 1555 1555 1.62 LINK O3' PDU A 23 P PDU A 24 1555 1555 1.61 LINK P PDU A 23 O3' DC A 22 1555 1555 1.61
SITE 1 AC1 2 DA A 1 DC A 18 SITE 1 AC2 5 DA A 1 DG A 2 DA A 3 PDU A 17 SITE 2 AC2 5 PDU A 19 SITE 1 AC3 5 DG A 2 DA A 3 DC A 18 DCM A 20 SITE 2 AC3 5 DC B 13 SITE 1 AC4 5 DA A 3 DG A 4 DA A 5 PDU A 19 SITE 2 AC4 5 PDU A 21 SITE 1 AC5 8 DA A 3 DG A 4 DA A 5 DG A 6 SITE 2 AC5 8 DCM A 20 DC A 22 DC B 11 DT B 12 SITE 1 AC6 6 DA A 5 DG A 6 DA A 7 PDU A 21 SITE 2 AC6 6 PDU A 23 DC B 11 SITE 1 AC7 4 DG A 6 DA A 7 DC A 22 PDU A 24 SITE 1 AC8 3 DA A 7 DA A 8 PDU A 23
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