HEADER DNA 18-JUN-13 2RT8 TITLE STRUCTURE OF METALLO-DNA IN SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'); 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 DNA, METALLO-BASE-PAIR, T-HG(II)-T BASE-PAIR EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR H.YAMAGUCHI,J.SEBERA,J.KONDO,S.ODA,T.KOMURO,T.KAWAMURA,T.DAIRAKU, AUTHOR 2 Y.KONDO,I.OKAMOTO,A.ONO,J.V.BURDA,C.KOJIMA,V.SYCHROVSKY,Y.TANAKA REVDAT 1 05-MAR-14 2RT8 0 JRNL AUTH H.YAMAGUCHI,J.SEBERA,J.KONDO,S.ODA,T.KOMURO,T.KAWAMURA, JRNL AUTH 2 T.DAIRAKU,Y.KONDO,I.OKAMOTO,A.ONO,J.V.BURDA,C.KOJIMA, JRNL AUTH 3 V.SYCHROVSKY,Y.TANAKA JRNL TITL THE STRUCTURE OF METALLO-DNA WITH CONSECUTIVE JRNL TITL 2 THYMINE-HGII-THYMINE BASE PAIRS EXPLAINS POSITIVE ENTROPY JRNL TITL 3 FOR THE METALLO BASE PAIR FORMATION. JRNL REF NUCLEIC ACIDS RES. 2013 JRNL REFN ESSN 1362-4962 JRNL PMID 24371287 JRNL DOI 10.1093/NAR/GKT1344 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RT8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-13. REMARK 100 THE RCSB ID CODE IS RCSB150255. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.0 MM 5'-D(*CP*GP*CP*GP*TP*TP* REMARK 210 GP*TP*CP*C)-3'-1, 2.0 MM 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'- REMARK 210 2, 4.0 MM MERCURY(II) PERCHLORATE-3, 100 MM SODIUM PERCHLORATE-4, REMARK 210 100 % [U-100% 2H] D2O-5, 100% D2O; 2.0 MM 5'-D(*CP*GP*CP*GP*TP* REMARK 210 TP*GP*TP*CP*C)-3'-6, 2.0 MM 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)- REMARK 210 3'-7, 4.0 MM MERCURY(II) PERCHLORATE-8, 100 MM SODIUM PERCHLORATE REMARK 210 -9, 95 % H2O-10, 5 % [U-100% 2H] D2O-11, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX800 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851, SPARKY 3.1, REMARK 210 MARDIGRAS REMARK 210 METHOD USED : SIMMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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 DT A 6 C5 DT A 6 C7 0.037 REMARK 500 1 DT B 16 C5 DT B 16 C7 0.038 REMARK 500 2 DT B 16 C5 DT B 16 C7 0.037 REMARK 500 3 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 3 DT B 16 C5 DT B 16 C7 0.038 REMARK 500 4 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 4 DT B 16 C5 DT B 16 C7 0.037 REMARK 500 5 DT A 6 C5 DT A 6 C7 0.037 REMARK 500 6 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 6 DT B 16 C5 DT B 16 C7 0.037 REMARK 500 7 DT B 16 C5 DT B 16 C7 0.038 REMARK 500 8 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 8 DT B 16 C5 DT B 16 C7 0.037 REMARK 500 9 DT B 16 C5 DT B 16 C7 0.037 REMARK 500 10 DT A 6 C5 DT A 6 C7 0.037 REMARK 500 10 DT A 8 C5 DT A 8 C7 0.037 REMARK 500 10 DT B 16 C5 DT B 16 C7 0.037 REMARK 500 11 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 11 DT B 16 C5 DT B 16 C7 0.037 REMARK 500 12 DT B 16 C5 DT B 16 C7 0.037 REMARK 500 13 DT B 16 C5 DT B 16 C7 0.037 REMARK 500 14 DT B 16 C5 DT B 16 C7 0.038 REMARK 500 15 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 15 DT B 16 C5 DT B 16 C7 0.038 REMARK 500 16 DT A 6 C5 DT A 6 C7 0.037 REMARK 500 16 DT B 16 C5 DT B 16 C7 0.038 REMARK 500 17 DT B 16 C5 DT B 16 C7 0.038 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG B 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 11 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG B 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DA B 13 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA B 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 13 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DC B 14 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT B 15 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT B 16 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC B 17 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG B 18 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DC B 19 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 20 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 20 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 2 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 630 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 HG A 102 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 6 N3 REMARK 620 2 DT B 15 N3 179.3 REMARK 620 3 DT A 6 O4 48.9 130.5 REMARK 620 4 DT B 15 O4 130.6 48.7 81.7 REMARK 620 5 DT A 6 O2 48.3 132.4 97.2 178.9 REMARK 620 6 DT B 15 O2 132.4 48.3 178.8 97.1 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 HG A 101 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 5 N3 REMARK 620 2 DT B 16 N3 177.4 REMARK 620 3 DT A 5 O4 49.3 128.1 REMARK 620 4 DT B 16 O4 128.3 49.1 78.9 REMARK 620 5 DT B 16 O2 134.8 47.8 175.9 97.0 REMARK 620 6 DT A 5 O2 47.6 135.0 96.9 175.9 87.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11528 RELATED DB: BMRB DBREF 2RT8 A 1 10 PDB 2RT8 2RT8 1 10 DBREF 2RT8 B 11 20 PDB 2RT8 2RT8 11 20 SEQRES 1 A 10 DC DG DC DG DT DT DG DT DC DC SEQRES 1 B 10 DG DG DA DC DT DT DC DG DC DG HET HG A 101 1 HET HG A 102 1 HETNAM HG MERCURY (II) ION FORMUL 3 HG 2(HG 2+) LINK N3 DT A 6 HG HG A 102 1555 1555 2.04 LINK N3 DT B 15 HG HG A 102 1555 1555 2.04 LINK N3 DT A 5 HG HG A 101 1555 1555 2.04 LINK N3 DT B 16 HG HG A 101 1555 1555 2.04 LINK O4 DT A 5 HG HG A 101 1555 1555 2.99 LINK O4 DT B 16 HG HG A 101 1555 1555 3.00 LINK O4 DT A 6 HG HG A 102 1555 1555 3.01 LINK O4 DT B 15 HG HG A 102 1555 1555 3.02 LINK O2 DT A 6 HG HG A 102 1555 1555 3.05 LINK O2 DT B 15 HG HG A 102 1555 1555 3.06 LINK O2 DT B 16 HG HG A 101 1555 1555 3.08 LINK O2 DT A 5 HG HG A 101 1555 1555 3.10 SITE 1 AC1 2 DT A 5 DT B 16 SITE 1 AC2 2 DT A 6 DT B 15 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 223 0 2 0 0 0 2 6 0 0 0 2 END