HEADER DNA 09-AUG-18 6ED9 TITLE NMR STRUCTURE FOR SP1 TRANSCRIPTION FACTOR DUPLEX 5'-D(TGGGCGGGA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*GP*GP*GP*CP*GP*GP*GP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*CP*CP*CP*GP*CP*CP*CP*A)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606 KEYWDS SP1 CONSENSUS SEQUENCE, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.V.DAVIS,M.HENNIG,D.P.ARYA REVDAT 3 14-JUN-23 6ED9 1 REMARK REVDAT 2 18-DEC-19 6ED9 1 REMARK REVDAT 1 14-AUG-19 6ED9 0 JRNL AUTH E.V.DAVIS,M.HENNIG,D.P.ARYA JRNL TITL AN NMR STRUCTURE DETERMINATION AND ANALYSIS OF FOUR SP1 JRNL TITL 2 CONSENSUS SEQUENCES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 14.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ED9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000235468. 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 : 30 MM NA+ REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 650 UM DNA, 25 MM SODIUM REMARK 210 CHLORIDE, 5 MM NA PHOSPHATE, 0.5 REMARK 210 MM EDTA, 100% D2O; 675 UM DNA, REMARK 210 25 MM SODIUM CHLORIDE, 5 MM NA REMARK 210 PHOSPHATE, 0.5 MM EDTA, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-13C HSQC; 2D 1H-1H NOESY; 2D REMARK 210 ECOSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.97, SPARKY, NMRPIPE, REMARK 210 3DNA, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 5 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC B 11 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 12 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC B 12 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC B 15 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC B 16 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC B 16 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 17 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DA B 18 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA B 18 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 18 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 9 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DT B 10 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC B 11 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DC B 12 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC B 12 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 281 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 DG A 4 0.06 SIDE CHAIN REMARK 500 1 DG A 6 0.06 SIDE CHAIN REMARK 500 1 DG B 14 0.10 SIDE CHAIN REMARK 500 3 DG A 4 0.06 SIDE CHAIN REMARK 500 3 DG A 7 0.07 SIDE CHAIN REMARK 500 3 DC B 11 0.07 SIDE CHAIN REMARK 500 3 DC B 13 0.06 SIDE CHAIN REMARK 500 3 DG B 14 0.07 SIDE CHAIN REMARK 500 4 DG A 4 0.07 SIDE CHAIN REMARK 500 4 DG A 7 0.07 SIDE CHAIN REMARK 500 4 DG B 14 0.07 SIDE CHAIN REMARK 500 5 DG A 7 0.10 SIDE CHAIN REMARK 500 5 DC B 13 0.09 SIDE CHAIN REMARK 500 6 DC A 5 0.06 SIDE CHAIN REMARK 500 6 DG A 7 0.07 SIDE CHAIN REMARK 500 6 DC B 13 0.08 SIDE CHAIN REMARK 500 7 DG B 14 0.05 SIDE CHAIN REMARK 500 9 DG A 4 0.06 SIDE CHAIN REMARK 500 9 DG B 14 0.09 SIDE CHAIN REMARK 500 10 DG A 7 0.06 SIDE CHAIN REMARK 500 10 DC B 15 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6DM7 RELATED DB: PDB REMARK 900 RELATED ID: 6DVT RELATED DB: PDB REMARK 900 RELATED ID: 6DXM RELATED DB: PDB REMARK 900 RELATED ID: 30506 RELATED DB: BMRB REMARK 900 NMR STRUCTURE FOR SP1 TRANSCRIPTION FACTOR DUPLEX 5'-D(TGGGCGGGA) DBREF 6ED9 A 1 9 PDB 6ED9 6ED9 1 9 DBREF 6ED9 B 10 18 PDB 6ED9 6ED9 10 18 SEQRES 1 A 9 DT DG DG DG DC DG DG DG DA SEQRES 1 B 9 DT DC DC DC DG DC DC DC DA 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