HEADER BINDING PROTEIN 26-APR-94 1OLB 1OLB 2 COMPND OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH 1OLB 3 COMPND 2 TRI-LYSINE 1OLB 4 SOURCE (SALMONELLA TYPHIMURIUM) 1OLB 5 AUTHOR J.TAME,A.J.WILKINSON 1OLB 6 REVDAT 1 31-JUL-94 1OLB 0 1OLB 7 JRNL AUTH J.TAME,G.N.MURSHUDOV,E.J.DODSON,T.K.NEIL, 1OLB 8 JRNL AUTH 2 G.G.DODSON,C.F.HIGGINS,A.J.WILKINSON 1OLB 9 JRNL TITL THE STRUCTURAL BASIS OF MULTISPECIFICITY IN THE 1OLB 10 JRNL TITL 2 OLIGOPEPTIDE-BINDING PROTEIN OPPA 1OLB 11 JRNL REF SCIENCE V. 264 1578 1994 1OLB 12 JRNL REFN ASTM SCIEAS US ISSN 0036-8075 0038 1OLB 13 REMARK 1 1OLB 14 REMARK 1 REFERENCE 1 1OLB 15 REMARK 1 AUTH I.D.GLOVER,R.DENNY,N.D.NGUTI,S.MCSWEENEY, 1OLB 16 REMARK 1 AUTH 2 A.THOMPSON,E.DODSON,A.J.WILKINSON,J.TAME 1OLB 17 REMARK 1 TITL STRUCTURE DETERMINATION OF OPPA AT 2.3 ANGSTROMS 1OLB 18 REMARK 1 TITL 2 RESOLUTION USING MULTIPLE WAVELENGTH ANOMALOUS 1OLB 19 REMARK 1 TITL 3 METHODS 1OLB 20 REMARK 1 REF TO BE PUBLISHED 1OLB 21 REMARK 1 REFN 0353 1OLB 22 REMARK 2 1OLB 23 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. 1OLB 24 REMARK 3 1OLB 25 REMARK 3 REFINEMENT. 1OLB 26 REMARK 3 PROGRAM PROLSQ 1OLB 27 REMARK 3 AUTHORS KONNERT,HENDRICKSON 1OLB 28 REMARK 3 R VALUE 0.172 1OLB 29 REMARK 3 RMSD BOND DISTANCES 0.018 ANGSTROMS 1OLB 30 REMARK 3 RMSD BOND ANGLE DISTANCES 0.034 ANGSTROMS 1OLB 31 REMARK 3 1OLB 32 REMARK 3 NUMBER OF REFLECTIONS 47801 1OLB 33 REMARK 3 RESOLUTION RANGE 10.0 - 1.80 ANGSTROMS 1OLB 34 REMARK 3 DATA CUTOFF 0.0 SIGMA(F) 1OLB 35 REMARK 3 PERCENT COMPLETION 84.1 1OLB 36 REMARK 3 1OLB 37 REMARK 3 NUMBER OF PROTEIN ATOMS 4165 1OLB 38 REMARK 3 NUMBER OF NUCLEIC ACID ATOMS 0 1OLB 39 REMARK 3 NUMBER OF SOLVENT ATOMS 432 1OLB 40 REMARK 3 NUMBER OF PEPTIDE LIGAND ATOMS 28 1OLB 41 REMARK 3 NUMBER OF URANIUM ATOMS 8 1OLB 42 REMARK 3 NUMBER OF URANYL OXYGEN ATOMS 10 1OLB 43 REMARK 3 NUMBER OF BUFFER (ACETATE) ATOMS 20 1OLB 44 REMARK 3 TOTAL NUMBER OF ATOMS 4663 1OLB 45 REMARK 3 1OLB 46 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF 1OLB 47 REMARK 3 SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED 1OLB 48 REMARK 3 STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE 1OLB 49 REMARK 3 WEIGHTS OF THE CORRESPONDING RESTRAINTS) 1OLB 50 REMARK 3 DISTANCE RESTRAINTS (ANGSTROMS) 1OLB 51 REMARK 3 BOND DISTANCE 0.018(0.025) 1OLB 52 REMARK 3 ANGLE DISTANCE 0.034(0.035) 1OLB 53 REMARK 3 PLANAR 1-4 DISTANCE 0.040(0.050) 1OLB 54 REMARK 3 PLANE RESTRAINT (ANGSTROMS) 0.017(0.030) 1OLB 55 REMARK 3 CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.129(0.150) 1OLB 56 REMARK 3 NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) 1OLB 57 REMARK 3 SINGLE TORSION CONTACT 0.171(0.300) 1OLB 58 REMARK 3 MULTIPLE TORSION CONTACT 0.271(0.300) 1OLB 59 REMARK 3 POSSIBLE HYDROGEN BOND 0.197(0.300) 1OLB 60 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) 1OLB 61 REMARK 3 PLANAR 3.275(7.000) 1OLB 62 REMARK 3 STAGGERED 17.473(20.00) 1OLB 63 REMARK 3 ORTHONORMAL 29.928(30.00) 1OLB 64 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS (ANGSTROMS**2) 1OLB 65 REMARK 3 MAIN-CHAIN BOND 2.688(4.000) 1OLB 66 REMARK 3 MAIN-CHAIN ANGLE 3.352(6.000) 1OLB 67 REMARK 3 SIDE-CHAIN BOND 6.026(8.000) 1OLB 68 REMARK 3 SIDE-CHAIN ANGLE 7.623(10.00) 1OLB 69 REMARK 3 1OLB 70 REMARK 3 PROGRAM PROLSQ MODIFIED BY E. DODSON. 1OLB 71 REMARK 4 1OLB 72 REMARK 4 THE OLIGOPEPTIDE BINDING PROTEIN OPPA IS SYNTHESISED AS A 1OLB 73 REMARK 4 542 AMINO ACID PRE-PROTEIN. THE 25 AMINO ACID SIGNAL 1OLB 74 REMARK 4 PEPTIDE IS CLEAVED FROM THE N-TERMINUS TO GIVE A 517 1OLB 75 REMARK 4 RESIDUE MATURE PROTEIN IN THE PERIPLASMIC SPACE. ALL 517 1OLB 76 REMARK 4 RESIDUES ARE CLEARLY VISIBLE IN THE ELECTRON DENSITY MAP. 1OLB 77 REMARK 5 1OLB 78 REMARK 5 FIVE ACETATE IONS HAVE BEEN MODELED INTO THE ELECTRON 1OLB 79 REMARK 5 DENSITY. ACETATE 1 IS FOUND AT THE SAME POSITION AS THE 1OLB 80 REMARK 5 CARBOXYL GROUP OF A BOUND TETRAPEPTIDE LIGAND. ACETATE 2 1OLB 81 REMARK 5 IS FOUND AT THE POSITION WHERE THE CARBOXYL GROUP OF A 1OLB 82 REMARK 5 BOUND PENTAPEPTIDE LIGAND IS BELIEVED TO LIE. THE 1OLB 83 REMARK 5 REMAINING ACETATES ARE FOUND AT THE SURFACE CLOSE TO URANYL 1OLB 84 REMARK 5 IONS AND HAVE RELATIVELY POOR DENSITY. SOLVENT STRUCTURE 1OLB 85 REMARK 5 AROUND THE URANYL IONS IS TENTATIVE. 1OLB 86 REMARK 6 1OLB 87 REMARK 6 FIVE OF THE EIGHT URANIUM IONS HAVE ASSOCIATED OXYGEN ATOMS 1OLB 88 REMARK 6 IN THE MODEL. THE GEOMETRY OF THESE URANYL IONS HAS NOT 1OLB 89 REMARK 6 BEEN RESTRAINED OR MANUALLY MODIFIED. THE (O-U-O)2+ ION 1OLB 90 REMARK 6 SHOULD BE LINEAR WITH AN O-U DISTANCE OF APPROXIMATELY 1.8 1OLB 91 REMARK 6 ANGSTROMS. 1OLB 92 REMARK 7 1OLB 93 REMARK 7 THE SEQUENCE OF THE MODEL AGREES WITH THE PREVIOUSLY 1OLB 94 REMARK 7 DETERMINED PROTEIN SEQUENCE. THE TRI-LYSINE LIGAND HAS 1OLB 95 REMARK 7 EXCELLENT DENSITY OVER ALL ATOMS. 1OLB 96 REMARK 8 1OLB 97 REMARK 8 CRYSTALS OF OPPA ARE ONLY OBTAINED IN THE PRESENCE OF 1OLB 98 REMARK 8 URANYL IONS WHICH BIND TO THE PROTEIN AND ARE RESPONSIBLE 1OLB 99 REMARK 8 FOR FORMING IMPORTANT CRYSTAL CONTACTS. TWO CRYSTAL FORMS 1OLB 100 REMARK 8 OF URANYL OPPA HAVE BEEN FOUND. THIS FILE DESCRIBES THE 1OLB 101 REMARK 8 STRUCTURE OF OPPA LIGANDED WITH TRI-LYSINE. THIS COMPLEX 1OLB 102 REMARK 8 CRYSTALLIZES WITH EIGHT URANYL IONS PER PROTEIN MOLECULE IN 1OLB 103 REMARK 8 SPACE-GROUP P 21 21 21. 1OLB 104 REMARK 9 1OLB 105 REMARK 9 OPPA CONTAINING CO-PURIFIED PEPTIDES CO-CRYSTALLIZED WITH 1OLB 106 REMARK 9 URANYL ACETATE GIVES CRYSTALS IN SPACE-GROUP P 21 21 2. 1OLB 107 REMARK 9 THIS STRUCTURE HAS BEEN REFINED SEPARATELY AND IS 1OLB 108 REMARK 9 PRESENTED IN PDB ENTRY 1OLA. 1OLB 109 REMARK 10 1OLB 110 REMARK 10 THERE ARE NO DISCONTINUITIES. THE PEPTIDE LIGAND IS A 1OLB 111 REMARK 10 SEPARATE CHAIN. 1OLB 112 SEQRES 1 A 517 ALA ASP VAL PRO ALA GLY VAL GLN LEU ALA ASP LYS GLN 1OLB 113 SEQRES 2 A 517 THR LEU VAL ARG ASN ASN GLY SER GLU VAL GLN SER LEU 1OLB 114 SEQRES 3 A 517 ASP PRO HIS LYS ILE GLU GLY VAL PRO GLU SER ASN VAL 1OLB 115 SEQRES 4 A 517 SER ARG ASP LEU PHE GLU GLY LEU LEU ILE SER ASP VAL 1OLB 116 SEQRES 5 A 517 GLU GLY HIS PRO SER PRO GLY VAL ALA GLU LYS TRP GLU 1OLB 117 SEQRES 6 A 517 ASN LYS ASP PHE LYS VAL TRP THR PHE HIS LEU ARG GLU 1OLB 118 SEQRES 7 A 517 ASN ALA LYS TRP SER ASP GLY THR PRO VAL THR ALA HIS 1OLB 119 SEQRES 8 A 517 ASP PHE VAL TYR SER TRP GLN ARG LEU ALA ASP PRO ASN 1OLB 120 SEQRES 9 A 517 THR ALA SER PRO TYR ALA SER TYR LEU GLN TYR GLY HIS 1OLB 121 SEQRES 10 A 517 ILE ALA ASN ILE ASP ASP ILE ILE ALA GLY LYS LYS PRO 1OLB 122 SEQRES 11 A 517 ALA THR ASP LEU GLY VAL LYS ALA LEU ASP ASP HIS THR 1OLB 123 SEQRES 12 A 517 PHE GLU VAL THR LEU SER GLU PRO VAL PRO TYR PHE TYR 1OLB 124 SEQRES 13 A 517 LYS LEU LEU VAL HIS PRO SER VAL SER PRO VAL PRO LYS 1OLB 125 SEQRES 14 A 517 SER ALA VAL GLU LYS PHE GLY ASP LYS TRP THR GLN PRO 1OLB 126 SEQRES 15 A 517 ALA ASN ILE VAL THR ASN GLY ALA TYR LYS LEU LYS ASN 1OLB 127 SEQRES 16 A 517 TRP VAL VAL ASN GLU ARG ILE VAL LEU GLU ARG ASN PRO 1OLB 128 SEQRES 17 A 517 GLN TYR TRP ASP ASN ALA LYS THR VAL ILE ASN GLN VAL 1OLB 129 SEQRES 18 A 517 THR TYR LEU PRO ILE SER SER GLU VAL THR ASP VAL ASN 1OLB 130 SEQRES 19 A 517 ARG TYR ARG SER GLY GLU ILE ASP MET THR TYR ASN ASN 1OLB 131 SEQRES 20 A 517 MET PRO ILE GLU LEU PHE GLN LYS LEU LYS LYS GLU ILE 1OLB 132 SEQRES 21 A 517 PRO ASN GLU VAL ARG VAL ASP PRO TYR LEU CYS THR TYR 1OLB 133 SEQRES 22 A 517 TYR TYR GLU ILE ASN ASN GLN LYS ALA PRO PHE ASN ASP 1OLB 134 SEQRES 23 A 517 VAL ARG VAL ARG THR ALA LEU LYS LEU ALA LEU ASP ARG 1OLB 135 SEQRES 24 A 517 ASP ILE ILE VAL ASN LYS VAL LYS ASN GLN GLY ASP LEU 1OLB 136 SEQRES 25 A 517 PRO ALA TYR SER TYR THR PRO PRO TYR THR ASP GLY ALA 1OLB 137 SEQRES 26 A 517 LYS LEU VAL GLU PRO GLU TRP PHE LYS TRP SER GLN GLN 1OLB 138 SEQRES 27 A 517 LYS ARG ASN GLU GLU ALA LYS LYS LEU LEU ALA GLU ALA 1OLB 139 SEQRES 28 A 517 GLY PHE THR ALA ASP LYS PRO LEU THR PHE ASP LEU LEU 1OLB 140 SEQRES 29 A 517 TYR ASN THR SER ASP LEU HIS LYS LYS LEU ALA ILE ALA 1OLB 141 SEQRES 30 A 517 VAL ALA SER ILE TRP LYS LYS ASN LEU GLY VAL ASN VAL 1OLB 142 SEQRES 31 A 517 ASN LEU GLU ASN GLN GLU TRP LYS THR PHE LEU ASP THR 1OLB 143 SEQRES 32 A 517 ARG HIS GLN GLY THR PHE ASP VAL ALA ARG ALA GLY TRP 1OLB 144 SEQRES 33 A 517 CYS ALA ASP TYR ASN GLU PRO THR SER PHE LEU ASN THR 1OLB 145 SEQRES 34 A 517 MET LEU SER ASP SER SER ASN ASN THR ALA HIS TYR LYS 1OLB 146 SEQRES 35 A 517 SER PRO ALA PHE ASP LYS LEU ILE ALA ASP THR LEU LYS 1OLB 147 SEQRES 36 A 517 VAL ALA ASP ASP THR GLN ARG SER GLU LEU TYR ALA LYS 1OLB 148 SEQRES 37 A 517 ALA GLU GLN GLN LEU ASP LYS ASP SER ALA ILE VAL PRO 1OLB 149 SEQRES 38 A 517 VAL TYR TYR TYR VAL ASN ALA ARG LEU VAL LYS PRO TRP 1OLB 150 SEQRES 39 A 517 VAL GLY GLY TYR THR GLY LYS ASP PRO LEU ASP ASN ILE 1OLB 151 SEQRES 40 A 517 TYR VAL LYS ASN LEU TYR ILE ILE LYS HIS 1OLB 152 SEQRES 1 B 3 LYS LYS LYS 1OLB 153 FTNOTE 1 1OLB 154 FTNOTE 1 CIS PROLINE - PRO A 283 1OLB 155 HET IUM C 1 3 URANYL(VI) ION 1OLB 156 HET IUM C 2 3 URANYL(VI) ION 1OLB 157 HET IUM C 3 3 URANYL(VI) ION 1OLB 158 HET IUM C 4 3 URANYL(VI) ION 1OLB 159 HET IUM C 5 3 URANYL(VI) ION 1OLB 160 HET IUM C 6 1 URANYL(VI) ION 1OLB 161 HET IUM C 7 1 URANYL(VI) ION 1OLB 162 HET IUM C 8 1 URANYL(VI) ION 1OLB 163 HET ACY E 1 4 ACETIC ACID 1OLB 164 HET ACY E 2 4 ACETIC ACID 1OLB 165 HET ACY E 3 4 ACETIC ACID 1OLB 166 HET ACY E 4 4 ACETIC ACID 1OLB 167 HET ACY E 5 4 ACETIC ACID 1OLB 168 FORMUL 3 IUM 8(O2 U1 ++) 1OLB 169 FORMUL 4 ACY 5(C2 H4 O2) 1OLB 170 FORMUL 5 HOH *432(H2 O1) 1OLB 171 HELIX 1 H01 VAL A 34 LEU A 43 1 1OLB 172 HELIX 2 H02 ALA A 90 ALA A 101 1 1OLB 173 HELIX 3 H03 TYR A 112 GLY A 116 1 1OLB 174 HELIX 4 H04 ILE A 121 ALA A 126 1 1OLB 175 HELIX 5 H05 LYS A 169 LYS A 174 1 1OLB 176 HELIX 6 H06 GLU A 229 SER A 238 1 1OLB 177 HELIX 7 H07 PHE A 253 GLU A 259 1 1OLB 178 HELIX 8 H08 VAL A 287 ALA A 296 1 1OLB 179 HELIX 9 H09 ARG A 299 VAL A 303 1 1OLB 180 HELIX 10 H10 GLN A 337 ALA A 351 1 1OLB 181 HELIX 11 H11 ASP A 369 LYS A 384 1 1OLB 182 HELIX 12 H12 TRP A 397 GLN A 406 1 1OLB 183 HELIX 13 H13 THR A 424 MET A 430 1 1OLB 184 HELIX 14 H14 PRO A 444 LYS A 455 1 1OLB 185 HELIX 15 H15 ASP A 459 ASP A 476 1 1OLB 186 SHEET 1 S1 7 LYS A 192 VAL A 197 0 1OLB 187 SHEET 2 S1 7 ARG A 201 ARG A 206 -1 1OLB 188 SHEET 3 S1 7 ASN A 219 LEU A 224 -1 1OLB 189 SHEET 4 S1 7 GLN A 13 ASN A 19 1 1OLB 190 SHEET 5 S1 7 MET A 243 THR A 244 1 1OLB 191 SHEET 6 S1 7 ASN A 487 LYS A 492 -1 1OLB 192 SHEET 7 S1 7 GLU A 263 ASP A 267 1 1OLB 193 SHEET 1 S2 4 LYS A 63 LYS A 67 0 1OLB 194 SHEET 2 S2 4 VAL A 71 LEU A 76 -1 1OLB 195 SHEET 3 S2 4 HIS A 142 LEU A 148 -1 1OLB 196 SHEET 4 S2 4 GLY A 135 SER A 149 -1 1OLB 197 SHEET 1 S3 5 ASN A 389 GLN A 395 0 1OLB 198 SHEET 2 S3 5 LEU A 359 THR A 367 1 1OLB 199 SHEET 3 S3 5 VAL A 411 ALA A 418 1 1OLB 200 SHEET 4 S3 5 LEU A 270 GLU A 276 -1 1OLB 201 SHEET 5 S3 5 VAL A 480 TYR A 485 -1 1OLB 202 SSBOND 1 CYS A 271 CYS A 417 1OLB 203 CRYST1 110.600 77.080 71.240 90.00 90.00 90.00 P 21 21 21 4 1OLB 204 ORIGX1 1.000000 0.000000 0.000000 0.00000 1OLB 205 ORIGX2 0.000000 1.000000 0.000000 0.00000 1OLB 206 ORIGX3 0.000000 0.000000 1.000000 0.00000 1OLB 207 SCALE1 0.009042 0.000000 0.000000 0.00000 1OLB 208 SCALE2 0.000000 0.012974 0.000000 0.00000 1OLB 209 SCALE3 0.000000 0.000000 0.014037 0.00000 1OLB 210