HEADER DNA 20-MAY-98 1SKP TITLE NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS TITLE 2 SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 TITLE 3 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIGMA-K RNA POLYMERASE CONSENSUS SEQUENCE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SIGMA-K RNA POLYMERASE CONSENSUS SEQUENCE; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS PROMOTER SEQUENCE, DNA EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR M.TONELLI,E.RAGG,A.M.BIANUCCI,K.LESIAK,T.L.JAMES REVDAT 4 02-MAR-22 1SKP 1 REMARK REVDAT 3 24-FEB-09 1SKP 1 VERSN REVDAT 2 01-APR-03 1SKP 1 JRNL REVDAT 1 13-JAN-99 1SKP 0 JRNL AUTH M.TONELLI,E.RAGG,A.M.BIANUCCI,K.LESIAK,T.L.JAMES JRNL TITL NUCLEAR MAGNETIC RESONANCE STRUCTURE OF D(GCATATGATAG). JRNL TITL 2 D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS JRNL TITL 3 RECOGNIZED BY SIGMA K RNA POLYMERASE. JRNL REF BIOCHEMISTRY V. 37 11745 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9718297 JRNL DOI 10.1021/BI980481N REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : PEARLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 BIOCHEMISTRY CITATION ABOVE. MODEL 1 : REFINED BY RMD FROM A-DNA REMARK 3 MODEL 2 : REFINED BY RMD FROM B-DNA MODEL 3 : REFINED BY RMC REMARK 3 FROM A-DNA MODEL 4 : REFINED BY RMC FROM B-DNA REMARK 4 REMARK 4 1SKP 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_1000176401. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.5 M REMARK 210 PRESSURE : 1 ATMOSPHERE REMARK 210 SAMPLE CONTENTS : H2O AND D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS, AMBER, DNAMINICARLO REMARK 210 METHOD USED : MOLECULAR DYNAMIC (RMD) AND REMARK 210 MONTE CARLO (RMC) CALCULATIONS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : CONVERGENCE, R FACTORS, ENERGIES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: STRUCTURE DETERMINED WITH HOMONUCLEAR NMR METHODS. 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 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 DC A 2 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DT A 4 C4 - C5 - C7 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -7.7 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 8 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 13 C6 - C5 - C7 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DT B 15 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA B 17 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DA B 17 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 17 C5 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT B 20 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 4 C4 - C5 - C7 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -7.7 DEGREES REMARK 500 2 DA A 5 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DA A 8 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DA A 10 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DT B 13 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DT B 15 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DA B 17 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA B 17 C5 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT B 20 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DG B 21 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DC B 22 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DG A 1 C3' - O3' - P ANGL. DEV. = 11.8 DEGREES REMARK 500 4 DG A 1 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 4 DG A 1 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES 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 DT A 4 0.12 SIDE CHAIN REMARK 500 1 DA A 10 0.07 SIDE CHAIN REMARK 500 1 DG A 11 0.06 SIDE CHAIN REMARK 500 1 DA B 17 0.09 SIDE CHAIN REMARK 500 1 DG B 21 0.05 SIDE CHAIN REMARK 500 2 DT A 4 0.10 SIDE CHAIN REMARK 500 2 DG B 21 0.05 SIDE CHAIN REMARK 500 2 DC B 22 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1SKP A 1 11 PDB 1SKP 1SKP 1 11 DBREF 1SKP B 12 22 PDB 1SKP 1SKP 12 22 SEQRES 1 A 11 DG DC DA DT DA DT DG DA DT DA DG SEQRES 1 B 11 DC DT DA DT DC DA DT DA DT DG DC 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