PDB Short entry for 5KIB HEADER DNA 16-JUN-16 5KIB TITLE STRUCTURAL IMPACT OF SINGLE RIBONUCLEOTIDES IN DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS DNA, RNA, RIBONUCLEOTIDES EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.EVICH,A.M.SPRING-CONNELL,F.STORICI,M.W.GERMANN REVDAT 4 01-MAY-24 5KIB 1 COMPND REMARK REVDAT 3 02-NOV-16 5KIB 1 JRNL REVDAT 2 21-SEP-16 5KIB 1 JRNL REVDAT 1 24-AUG-16 5KIB 0 JRNL AUTH M.EVICH,A.M.SPRING-CONNELL,F.STORICI,M.W.GERMANN JRNL TITL STRUCTURAL IMPACT OF SINGLE RIBONUCLEOTIDE RESIDUES IN DNA. JRNL REF CHEMBIOCHEM V. 17 1968 2016 JRNL REFN ESSN 1439-7633 JRNL PMID 27504600 JRNL DOI 10.1002/CBIC.201600385 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CORMA, MARDIGRAS REMARK 3 AUTHORS : THOMAS JAMES (CORMA), THOMAS JAMES (MARDIGRAS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5KIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222280. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 294; 294 REMARK 210 PH : 6.6; 7.0 REMARK 210 IONIC STRENGTH : 110; 110 REMARK 210 PRESSURE : AMBIENT ATM; AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1 MM DNA/RNA (5'-D(*TP*TP*AP*G) REMARK 210 -R(P*G)-D(P*CP*CP*TP*G)-3'), 1 MM DNA (5'-D(*CP*AP*GP*GP*CP*CP* REMARK 210 TP*AP*A)-3'), 100 % 100% DEUTERIUM D2O, 100 MM SODIUM CHLORIDE, REMARK 210 10 MM SODIUM PHOSPHATE, 100% D2O; 1 MM DNA/RNA (5'-D(*TP*TP*AP*G) REMARK 210 -R(P*G)-D(P*CP*CP*TP*G)-3'), 1 MM DNA (5'-D(*CP*AP*GP*GP*CP*CP* REMARK 210 TP*AP*A)-3'), 100 MM SODIUM CHLORIDE, 10 MM SODIUM PHOSPHATE, 10 REMARK 210 % 100% DEUTERIUM D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY 250 MS; 2D LOW FLIP REMARK 210 COSY; 2D 1H-13C HSQC; 2D REMARK 210 CONSTANT TIME NOESY; 2D 1H-31P REMARK 210 CORR; 2D NOESY 150 MS; 1D 1H; 1D REMARK 210 31P; 1D 1H 1-1 JUMP AND RETURN REMARK 210 SPECTROMETER FIELD STRENGTH : 600 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 : AMBER 9, SPARKY 3.33, TOPSPIN REMARK 210 METHOD USED : MATRIX RELAXATION, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 6 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA B 11 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA B 11 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA B 11 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA B 17 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 17 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA B 18 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 18 C4 - C5 - C6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA B 18 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 18 N1 - C6 - N6 ANGL. DEV. = -6.4 DEGREES REMARK 500 2 DT A 1 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT A 1 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DA B 11 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DA B 11 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA B 11 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC B 15 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT B 16 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DA B 17 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DA B 18 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA B 18 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DA B 18 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA B 18 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 251 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 DC A 6 0.12 SIDE CHAIN REMARK 500 1 DG A 9 0.09 SIDE CHAIN REMARK 500 1 DC B 10 0.08 SIDE CHAIN REMARK 500 1 DG B 12 0.08 SIDE CHAIN REMARK 500 1 DG B 13 0.07 SIDE CHAIN REMARK 500 1 DA B 17 0.06 SIDE CHAIN REMARK 500 2 DC A 6 0.14 SIDE CHAIN REMARK 500 2 DG A 9 0.06 SIDE CHAIN REMARK 500 2 DG B 12 0.06 SIDE CHAIN REMARK 500 2 DG B 13 0.06 SIDE CHAIN REMARK 500 2 DC B 15 0.07 SIDE CHAIN REMARK 500 2 DA B 18 0.06 SIDE CHAIN REMARK 500 3 DC A 6 0.11 SIDE CHAIN REMARK 500 3 DG B 12 0.09 SIDE CHAIN REMARK 500 3 DG B 13 0.08 SIDE CHAIN REMARK 500 3 DC B 15 0.08 SIDE CHAIN REMARK 500 3 DA B 17 0.05 SIDE CHAIN REMARK 500 3 DA B 18 0.08 SIDE CHAIN REMARK 500 4 DC A 6 0.14 SIDE CHAIN REMARK 500 4 DC B 10 0.08 SIDE CHAIN REMARK 500 4 DG B 12 0.08 SIDE CHAIN REMARK 500 4 DG B 13 0.06 SIDE CHAIN REMARK 500 4 DC B 15 0.08 SIDE CHAIN REMARK 500 5 DC A 6 0.11 SIDE CHAIN REMARK 500 5 DC B 10 0.08 SIDE CHAIN REMARK 500 5 DG B 12 0.06 SIDE CHAIN REMARK 500 6 DC A 6 0.16 SIDE CHAIN REMARK 500 6 DC B 10 0.07 SIDE CHAIN REMARK 500 6 DG B 12 0.06 SIDE CHAIN REMARK 500 6 DC B 15 0.06 SIDE CHAIN REMARK 500 6 DA B 17 0.05 SIDE CHAIN REMARK 500 6 DA B 18 0.07 SIDE CHAIN REMARK 500 7 DG A 4 0.10 SIDE CHAIN REMARK 500 7 DC A 6 0.12 SIDE CHAIN REMARK 500 7 DC A 7 0.07 SIDE CHAIN REMARK 500 7 DC B 10 0.08 SIDE CHAIN REMARK 500 7 DA B 11 0.06 SIDE CHAIN REMARK 500 7 DG B 12 0.07 SIDE CHAIN REMARK 500 7 DG B 13 0.07 SIDE CHAIN REMARK 500 7 DA B 17 0.07 SIDE CHAIN REMARK 500 7 DA B 18 0.09 SIDE CHAIN REMARK 500 8 DG A 4 0.10 SIDE CHAIN REMARK 500 8 G A 5 0.06 SIDE CHAIN REMARK 500 8 DC A 6 0.12 SIDE CHAIN REMARK 500 8 DC B 10 0.08 SIDE CHAIN REMARK 500 8 DG B 12 0.07 SIDE CHAIN REMARK 500 8 DC B 15 0.07 SIDE CHAIN REMARK 500 8 DA B 17 0.06 SIDE CHAIN REMARK 500 9 DG A 4 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 61 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30114 RELATED DB: BMRB REMARK 900 RELATED ID: 5KGV RELATED DB: PDB REMARK 900 RELATED ID: 5KI7 RELATED DB: PDB REMARK 900 RELATED ID: 5KIE RELATED DB: PDB REMARK 900 RELATED ID: 5KIF RELATED DB: PDB REMARK 900 RELATED ID: 5KIH RELATED DB: PDB DBREF 5KIB A 1 9 PDB 5KIB 5KIB 1 9 DBREF 5KIB B 10 18 PDB 5KIB 5KIB 10 18 SEQRES 1 A 9 DT DT DA DG G DC DC DT DG SEQRES 1 B 9 DC DA DG DG DC DC DT DA 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