HEADER DNA 31-JUL-12 2LWH TITLE NMR STRUCTURE OF THE SELF-COMPLEMENTARY 10 MER DNA DUPLEX 5'- TITLE 2 GGATATATCC-3' IN COMPLEX WITH NETROPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3'); COMPND 3 CHAIN: 1, 2; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS MICROSTRUCTURE, INDUCED DNA BINDING, DNA MINOR GROOVE VARIATIONS, DNA EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR M.RETTIG,M.W.GERMANN,W.WILSON,S.WANG REVDAT 3 26-JUL-17 2LWH 1 REMARK ATOM REVDAT 2 20-FEB-13 2LWH 1 JRNL REVDAT 1 23-JAN-13 2LWH 0 JRNL AUTH M.RETTIG,M.W.GERMANN,S.WANG,W.D.WILSON JRNL TITL MOLECULAR BASIS FOR SEQUENCE-DEPENDENT INDUCED DNA BENDING. JRNL REF CHEMBIOCHEM V. 14 323 2013 JRNL REFN ISSN 1439-4227 JRNL PMID 23355266 JRNL DOI 10.1002/CBIC.201200706 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9, AMBER 9 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN (AMBER), CASE, DARDEN, REMARK 3 CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, AND REMARK 3 KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000102918. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9 MM DNA (5' REMARK 210 -D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3'), 0.9 MM NETROPSIN, 100% REMARK 210 D2O; 0.9 MM DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3'), 0.9 MM REMARK 210 NETROPSIN, 90% H2O/10% D2O; 0.6 MM DNA (5'-D(*GP*GP*AP*TP*AP*TP* REMARK 210 AP*TP*CP*C)-3'), 9 MG/ML PF1 PHAGE, 0.6 MM NETROPSIN, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 9500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 418 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2391 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 2 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 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 1 3 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA 1 3 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA 1 3 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT 1 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT 1 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA 1 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA 1 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA 1 5 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT 1 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA 1 7 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA 1 7 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT 1 8 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC 1 10 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA 2 13 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA 2 13 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA 2 13 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DT 2 14 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA 2 15 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA 2 15 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA 2 15 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DT 2 16 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA 2 17 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA 2 17 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA 2 17 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DT 2 18 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC 2 19 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC 2 20 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DA 1 3 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DA 1 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA 1 3 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT 1 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DA 1 5 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DA 1 5 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DT 1 6 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DA 1 7 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA 1 7 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DT 1 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC 1 9 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC 1 9 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DC 1 10 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DA 2 13 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA 2 13 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA 2 13 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DT 2 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA 2 15 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA 2 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA 2 15 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 2 DT 2 16 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA 2 17 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DA 2 17 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 322 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 1 3 0.07 SIDE CHAIN REMARK 500 1 DT 1 6 0.07 SIDE CHAIN REMARK 500 1 DT 1 8 0.06 SIDE CHAIN REMARK 500 1 DT 2 16 0.07 SIDE CHAIN REMARK 500 1 DA 2 17 0.09 SIDE CHAIN REMARK 500 2 DA 1 5 0.06 SIDE CHAIN REMARK 500 2 DT 1 8 0.08 SIDE CHAIN REMARK 500 2 DG 2 11 0.05 SIDE CHAIN REMARK 500 2 DT 2 16 0.07 SIDE CHAIN REMARK 500 2 DA 2 17 0.06 SIDE CHAIN REMARK 500 3 DG 1 1 0.07 SIDE CHAIN REMARK 500 3 DA 1 3 0.07 SIDE CHAIN REMARK 500 3 DT 1 6 0.08 SIDE CHAIN REMARK 500 3 DT 1 8 0.07 SIDE CHAIN REMARK 500 3 DA 2 13 0.06 SIDE CHAIN REMARK 500 3 DT 2 14 0.08 SIDE CHAIN REMARK 500 3 DA 2 17 0.08 SIDE CHAIN REMARK 500 4 DT 1 6 0.08 SIDE CHAIN REMARK 500 4 DT 1 8 0.08 SIDE CHAIN REMARK 500 4 DG 2 12 0.06 SIDE CHAIN REMARK 500 5 DG 1 1 0.07 SIDE CHAIN REMARK 500 5 DA 1 3 0.06 SIDE CHAIN REMARK 500 5 DT 1 6 0.09 SIDE CHAIN REMARK 500 5 DA 2 13 0.07 SIDE CHAIN REMARK 500 5 DT 2 14 0.09 SIDE CHAIN REMARK 500 5 DA 2 17 0.08 SIDE CHAIN REMARK 500 6 DA 1 5 0.07 SIDE CHAIN REMARK 500 6 DT 1 6 0.11 SIDE CHAIN REMARK 500 6 DT 1 8 0.07 SIDE CHAIN REMARK 500 6 DG 2 12 0.07 SIDE CHAIN REMARK 500 6 DA 2 13 0.06 SIDE CHAIN REMARK 500 7 DA 1 5 0.08 SIDE CHAIN REMARK 500 7 DT 1 6 0.11 SIDE CHAIN REMARK 500 7 DT 1 8 0.07 SIDE CHAIN REMARK 500 7 DG 2 11 0.07 SIDE CHAIN REMARK 500 7 DT 2 14 0.08 SIDE CHAIN REMARK 500 7 DT 2 16 0.07 SIDE CHAIN REMARK 500 8 DT 1 6 0.10 SIDE CHAIN REMARK 500 8 DT 1 8 0.07 SIDE CHAIN REMARK 500 8 DT 2 16 0.10 SIDE CHAIN REMARK 500 8 DA 2 17 0.07 SIDE CHAIN REMARK 500 9 DA 1 5 0.07 SIDE CHAIN REMARK 500 9 DT 1 6 0.07 SIDE CHAIN REMARK 500 9 DT 2 16 0.07 SIDE CHAIN REMARK 500 9 DA 2 17 0.07 SIDE CHAIN REMARK 500 10 DT 1 6 0.09 SIDE CHAIN REMARK 500 10 DT 1 8 0.10 SIDE CHAIN REMARK 500 10 DG 2 11 0.11 SIDE CHAIN REMARK 500 10 DG 2 12 0.07 SIDE CHAIN REMARK 500 10 DT 2 14 0.06 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 61 PLANE DEVIATIONS. 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 NT 1 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LWG RELATED DB: PDB REMARK 900 THE FREE DNA WITHOUT NETROPSIN. REMARK 900 RELATED ID: 18626 RELATED DB: BMRB DBREF 2LWH 1 1 10 PDB 2LWH 2LWH 1 10 DBREF 2LWH 2 11 20 PDB 2LWH 2LWH 11 20 SEQRES 1 1 10 DG DG DA DT DA DT DA DT DC DC SEQRES 1 2 10 DG DG DA DT DA DT DA DT DC DC HET NT 1 101 59 HETNAM NT NETROPSIN FORMUL 3 NT C18 H26 N10 O3 SITE 1 AC1 12 DT 1 4 DA 1 5 DT 1 6 DA 1 7 SITE 2 AC1 12 DT 1 8 DC 1 9 DT 2 14 DA 2 15 SITE 3 AC1 12 DT 2 16 DA 2 17 DT 2 18 DC 2 19 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 225 0 1 0 0 0 3 6 0 0 0 2 END