HEADER IMMUNE SYSTEM/DNA 22-MAY-06 2H3C TITLE STRUCTURAL BASIS FOR NUCLEIC ACID AND TOXIN RECOGNITION OF THE TITLE 2 BACTERIAL ANTITOXIN CCDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3'; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3'; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CCDA; COMPND 11 CHAIN: A, B; COMPND 12 SYNONYM: CCDA CONFORMER B; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBBON-HELIX-HELIX, IMMUNE SYSTEM-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.MADL,L.VAN MELDEREN,M.RESPONDEK,M.OBERER,W.KELLER,K.ZANGGER REVDAT 3 10-NOV-21 2H3C 1 REMARK SEQADV REVDAT 2 24-FEB-09 2H3C 1 VERSN REVDAT 1 21-NOV-06 2H3C 0 JRNL AUTH T.MADL,L.VAN MELDEREN,N.MINE,M.RESPONDEK,M.OBERER,W.KELLER, JRNL AUTH 2 L.KHATAI,K.ZANGGER JRNL TITL STRUCTURAL BASIS FOR NUCLEIC ACID AND TOXIN RECOGNITION OF JRNL TITL 2 THE BACTERIAL ANTITOXIN CCDA JRNL REF J.MOL.BIOL. V. 364 170 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 17007877 JRNL DOI 10.1016/J.JMB.2006.08.082 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER (CNS), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2H3C COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000037877. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM CCDA U15N, 13C IN COMPLEX REMARK 210 WITH A 12 BP CCD OP DNA FRAGMENT; REMARK 210 20MM PHOSPHATE BUFFER, 90% H2O, REMARK 210 10% D2O; 0.5MM CCDA U15N, 13C IN REMARK 210 COMPLEX WITH A 12 BP CCD OP DNA REMARK 210 FRAGMENT; 20MM PHOSPHATE BUFFER, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, VNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HZ1 LYS A 2 OG SER B 111 1.29 REMARK 500 HZ3 LYS A 45 OD1 ASN A 69 1.33 REMARK 500 O ARG B 143 HZ3 LYS B 145 1.38 REMARK 500 OE1 GLU B 142 HZ2 LYS B 145 1.38 REMARK 500 OG SER A 64 HH12 ARG B 143 1.40 REMARK 500 HZ1 LYS A 70 OE2 GLU B 142 1.40 REMARK 500 OE1 GLU A 35 HH TYR B 120 1.47 REMARK 500 HE ARG A 38 O ARG A 40 1.48 REMARK 500 HH21 ARG A 40 OD2 ASP B 167 1.48 REMARK 500 O LYS A 70 HH11 ARG B 138 1.48 REMARK 500 O VAL A 9 H GLN B 103 1.53 REMARK 500 O VAL A 28 H MET A 32 1.53 REMARK 500 OE2 GLU A 47 HH22 ARG A 57 1.54 REMARK 500 O GLY B 126 HG1 THR B 130 1.55 REMARK 500 OG1 THR A 6 HH11 ARG B 104 1.55 REMARK 500 HH TYR A 20 OD2 ASP A 67 1.55 REMARK 500 HH22 ARG A 43 OE1 GLU B 150 1.56 REMARK 500 O ASN A 23 H SER A 25 1.56 REMARK 500 O GLY A 26 HG1 THR A 30 1.56 REMARK 500 HE ARG A 57 OD2 ASP A 71 1.57 REMARK 500 O VAL B 128 H MET B 132 1.58 REMARK 500 O ASP A 67 H ARG B 140 1.60 REMARK 500 O LEU A 27 H THR A 31 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 LYS A 2 140.73 71.82 REMARK 500 1 VAL A 9 -120.49 -99.03 REMARK 500 1 ASP A 10 -85.09 157.61 REMARK 500 1 SER A 13 -23.54 61.52 REMARK 500 1 ASP A 21 35.92 157.18 REMARK 500 1 VAL A 22 96.00 -167.56 REMARK 500 1 ASN A 23 66.23 -67.26 REMARK 500 1 ILE A 24 -6.83 36.34 REMARK 500 1 LEU A 39 37.95 37.44 REMARK 500 1 ARG A 40 109.99 -177.98 REMARK 500 1 ALA A 41 96.19 79.59 REMARK 500 1 VAL A 46 104.87 -160.42 REMARK 500 1 GLU A 47 -67.05 -108.73 REMARK 500 1 GLU A 50 -94.77 41.06 REMARK 500 1 MET A 52 -53.12 72.25 REMARK 500 1 VAL A 55 -61.80 -152.60 REMARK 500 1 ALA A 56 97.81 68.10 REMARK 500 1 GLU A 60 -56.51 -144.53 REMARK 500 1 SER A 64 -166.45 84.60 REMARK 500 1 PHE A 65 -102.33 54.99 REMARK 500 1 ALA A 66 64.47 -158.02 REMARK 500 1 ASP A 67 -61.59 -155.38 REMARK 500 1 GLU A 68 173.01 61.18 REMARK 500 1 VAL B 109 -131.78 -82.75 REMARK 500 1 ASP B 110 -3.39 86.34 REMARK 500 1 SER B 111 -59.27 -137.04 REMARK 500 1 ASP B 112 -91.60 -46.15 REMARK 500 1 SER B 113 36.53 179.11 REMARK 500 1 ASP B 121 15.82 160.21 REMARK 500 1 ASN B 123 -97.64 -56.58 REMARK 500 1 ILE B 124 -1.28 -142.73 REMARK 500 1 LEU B 139 100.69 -10.49 REMARK 500 1 ARG B 140 76.39 -153.99 REMARK 500 1 ALA B 141 112.75 -33.64 REMARK 500 1 TRP B 144 71.87 63.05 REMARK 500 1 ASN B 148 53.55 179.36 REMARK 500 1 MET B 152 -141.16 -110.78 REMARK 500 1 VAL B 153 143.74 80.96 REMARK 500 1 VAL B 155 54.26 178.72 REMARK 500 1 ILE B 159 -41.39 -174.49 REMARK 500 1 GLU B 160 -77.94 -83.57 REMARK 500 1 MET B 161 -67.94 -178.64 REMARK 500 1 ALA B 166 -116.86 -162.35 REMARK 500 1 GLU B 168 46.44 37.70 REMARK 500 2 VAL A 9 -146.00 -81.90 REMARK 500 2 ASP A 10 -10.97 87.82 REMARK 500 2 ASP A 12 -86.41 -51.68 REMARK 500 2 SER A 13 44.56 178.77 REMARK 500 2 ASP A 21 26.24 152.88 REMARK 500 2 ASN A 23 -92.01 -54.78 REMARK 500 REMARK 500 THIS ENTRY HAS 919 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2H3A RELATED DB: PDB DBREF 2H3C A 1 72 UNP Q9S0Z5 Q9S0Z5_ECOLI 1 72 DBREF 2H3C B 101 172 UNP Q9S0Z5 Q9S0Z5_ECOLI 1 72 DBREF 2H3C C 173 185 PDB 2H3C 2H3C 173 185 DBREF 2H3C D 186 198 PDB 2H3C 2H3C 186 198 SEQADV 2H3C LYS A 70 UNP Q9S0Z5 ARG 70 ENGINEERED MUTATION SEQADV 2H3C LYS B 170 UNP Q9S0Z5 ARG 70 ENGINEERED MUTATION SEQRES 1 C 13 DA DT DA DT DG DT DA DT DA DC DC DC DG SEQRES 1 D 13 DT DC DG DG DG DT DA DT DA DC DA DT DA SEQRES 1 A 72 MET LYS GLN ARG ILE THR VAL THR VAL ASP SER ASP SER SEQRES 2 A 72 TYR GLN LEU LEU LYS ALA TYR ASP VAL ASN ILE SER GLY SEQRES 3 A 72 LEU VAL SER THR THR MET GLN ASN GLU ALA ARG ARG LEU SEQRES 4 A 72 ARG ALA GLU ARG TRP LYS VAL GLU ASN GLN GLU GLY MET SEQRES 5 A 72 VAL GLU VAL ALA ARG PHE ILE GLU MET ASN GLY SER PHE SEQRES 6 A 72 ALA ASP GLU ASN LYS ASP TRP SEQRES 1 B 72 MET LYS GLN ARG ILE THR VAL THR VAL ASP SER ASP SER SEQRES 2 B 72 TYR GLN LEU LEU LYS ALA TYR ASP VAL ASN ILE SER GLY SEQRES 3 B 72 LEU VAL SER THR THR MET GLN ASN GLU ALA ARG ARG LEU SEQRES 4 B 72 ARG ALA GLU ARG TRP LYS VAL GLU ASN GLN GLU GLY MET SEQRES 5 B 72 VAL GLU VAL ALA ARG PHE ILE GLU MET ASN GLY SER PHE SEQRES 6 B 72 ALA ASP GLU ASN LYS ASP TRP HELIX 1 1 SER A 13 ASP A 21 1 9 HELIX 2 2 ILE A 24 LEU A 39 1 16 HELIX 3 3 SER B 113 ASP B 121 1 9 HELIX 4 4 ILE B 124 LEU B 139 1 16 SHEET 1 A 2 GLN A 3 VAL A 9 0 SHEET 2 A 2 GLN B 103 VAL B 109 -1 O GLN B 103 N VAL A 9 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