HEADER IMMUNE SYSTEM/DNA 22-MAY-06 2H3A 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 A; 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 2H3A 1 REMARK SEQADV REVDAT 2 24-FEB-09 2H3A 1 VERSN REVDAT 1 21-NOV-06 2H3A 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 2H3A 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_1000037875. 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 U-15N, 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 U-15N, 13C REMARK 210 IN COMPLEX WITH A 12 BP CCD OP REMARK 210 DNA FRAGMENT; 20MM PHOSPHATE REMARK 210 BUFFER, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; DRX 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 1.31 REMARK 500 O TRP B 144 HZ2 LYS B 145 1.34 REMARK 500 OH TYR A 14 HZ2 LYS A 18 1.37 REMARK 500 O ARG A 43 HZ2 LYS A 45 1.37 REMARK 500 OE1 GLN A 15 HZ1 LYS A 18 1.38 REMARK 500 O ALA A 56 HH11 ARG A 57 1.45 REMARK 500 HZ3 LYS A 2 OD2 ASP B 110 1.45 REMARK 500 O LEU B 139 HE ARG B 140 1.45 REMARK 500 HZ2 LYS A 70 OXT TRP A 72 1.47 REMARK 500 HH11 ARG B 138 O ALA B 141 1.48 REMARK 500 OE2 GLU A 42 HZ3 LYS A 45 1.48 REMARK 500 O SER B 125 HG SER B 129 1.49 REMARK 500 O VAL B 122 H ILE B 124 1.52 REMARK 500 HH TYR A 20 O ALA B 136 1.52 REMARK 500 O ASP B 112 HG SER B 113 1.55 REMARK 500 O VAL B 128 H MET B 132 1.56 REMARK 500 O LEU A 27 HG1 THR A 31 1.57 REMARK 500 O VAL A 9 H GLN B 103 1.57 REMARK 500 O THR B 131 H GLU B 135 1.58 REMARK 500 O LEU A 27 H THR A 31 1.58 REMARK 500 O MET A 32 H ALA A 36 1.58 REMARK 500 OD2 ASP A 10 HG SER A 11 1.59 REMARK 500 HG1 THR A 30 OD2 ASP B 112 1.59 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 THR A 8 67.17 -69.77 REMARK 500 1 VAL A 9 -132.32 -106.09 REMARK 500 1 ASP A 10 -87.16 148.34 REMARK 500 1 SER A 13 -18.50 65.25 REMARK 500 1 ASP A 21 35.15 163.92 REMARK 500 1 ASN A 23 13.44 -60.71 REMARK 500 1 ILE A 24 -5.81 65.12 REMARK 500 1 VAL A 28 -73.40 -40.10 REMARK 500 1 LEU A 39 82.15 12.29 REMARK 500 1 ALA A 41 138.33 168.39 REMARK 500 1 ASN A 48 47.62 -156.75 REMARK 500 1 VAL A 55 -79.74 -132.42 REMARK 500 1 ALA A 56 94.97 56.67 REMARK 500 1 PHE A 58 97.15 -170.46 REMARK 500 1 ILE A 59 -130.68 -92.89 REMARK 500 1 ASP A 67 -76.25 -96.08 REMARK 500 1 GLU A 68 -176.02 65.43 REMARK 500 1 ASN A 69 -99.11 -178.19 REMARK 500 1 LYS A 70 -33.02 178.72 REMARK 500 1 ASP A 71 80.37 64.80 REMARK 500 1 THR B 108 84.30 -68.13 REMARK 500 1 VAL B 109 -116.65 -72.56 REMARK 500 1 ASP B 110 -7.48 75.63 REMARK 500 1 SER B 111 -69.43 -127.18 REMARK 500 1 ASP B 112 -78.28 -42.36 REMARK 500 1 SER B 113 46.78 169.00 REMARK 500 1 ASP B 121 22.82 157.04 REMARK 500 1 ASN B 123 56.74 -64.54 REMARK 500 1 ILE B 124 -11.64 44.66 REMARK 500 1 LEU B 139 70.68 37.16 REMARK 500 1 ARG B 140 -71.89 171.34 REMARK 500 1 ALA B 141 148.15 179.45 REMARK 500 1 TRP B 144 -151.43 -125.54 REMARK 500 1 MET B 152 67.01 -115.10 REMARK 500 1 VAL B 155 -122.38 -114.70 REMARK 500 1 ALA B 156 34.73 71.69 REMARK 500 1 PHE B 158 80.94 -151.32 REMARK 500 1 ILE B 159 -56.88 -148.92 REMARK 500 1 MET B 161 107.74 -163.21 REMARK 500 1 ASN B 162 -175.95 -176.53 REMARK 500 1 PHE B 165 129.95 -179.81 REMARK 500 1 GLU B 168 28.33 -145.69 REMARK 500 1 ASN B 169 -116.38 176.26 REMARK 500 1 LYS B 170 -33.11 168.29 REMARK 500 1 ASP B 171 88.87 98.05 REMARK 500 2 LYS A 2 112.92 -27.82 REMARK 500 2 VAL A 9 -162.07 -72.26 REMARK 500 2 ASP A 10 -23.59 84.70 REMARK 500 2 SER A 11 -75.52 -96.36 REMARK 500 2 ASP A 12 -87.69 -51.46 REMARK 500 REMARK 500 THIS ENTRY HAS 904 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2H3C RELATED DB: PDB DBREF 2H3A A 1 72 UNP Q9S0Z5 Q9S0Z5_ECOLI 1 72 DBREF 2H3A B 101 172 UNP Q9S0Z5 Q9S0Z5_ECOLI 1 72 DBREF 2H3A C 173 185 PDB 2H3A 2H3A 173 185 DBREF 2H3A D 186 198 PDB 2H3A 2H3A 186 198 SEQADV 2H3A LYS A 70 UNP Q9S0Z5 ARG 70 ENGINEERED MUTATION SEQADV 2H3A 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 ARG A 4 VAL A 9 0 SHEET 2 A 2 GLN B 103 THR B 108 -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