HEADER LYASE(CARBON-CARBON) 12-MAY-93 1RBL 1RBL 2 COMPND RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE 1RBL 3 COMPND 2 (RUBISCO) (E.C.4.1.1.39) 1RBL 4 SOURCE (SYNECHOCOCCUS, STRAIN PCC 6301) FORMERLY 1RBL 5 SOURCE 2 (ANACYSTIS NIDULANS) 1RBL 6 AUTHOR J.NEWMAN,S.GUTTERIDGE,C.-I.BRANDEN,T.A.JONES 1RBLA 1 REVDAT 2 08-MAR-95 1RBLA 1 AUTHOR JRNL 1RBLA 2 REVDAT 1 22-JUN-94 1RBL 0 1RBL 8 JRNL AUTH J.NEWMAN,C.-I.BRANDEN,T.A.JONES 1RBLA 3 JRNL TITL STRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1RBL 10 JRNL TITL 2 1,5 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE 1RBL 11 JRNL TITL 3 FROM SYNECHOCOCCUS PCC6301 1RBL 12 JRNL REF TO BE PUBLISHED 1RBL 13 JRNL REFN 0353 1RBL 14 REMARK 1 1RBL 15 REMARK 1 REFERENCE 1 1RBL 16 REMARK 1 AUTH J.NEWMAN,S.GUTTERIDGE 1RBL 17 REMARK 1 TITL THE X-RAY STRUCTURE OF SYNECHOCOCCUS RIBULOSE 1RBL 18 REMARK 1 TITL 2 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE ACTIVATED 1RBL 19 REMARK 1 TITL 3 QUATERNARY COMPLEX AT 2.2 ANGSTROMS RESOLUTION 1RBL 20 REMARK 1 REF TO BE PUBLISHED 1RBL 21 REMARK 1 REFN 0353 1RBL 22 REMARK 2 1RBL 23 REMARK 2 RESOLUTION. 2.2 ANGSTROMS. 1RBL 24 REMARK 3 1RBL 25 REMARK 3 REFINEMENT. 1RBL 26 REMARK 3 PROGRAM X-PLOR 1RBL 27 REMARK 3 AUTHORS BRUNGER 1RBL 28 REMARK 3 R VALUE 0.200 1RBL 29 REMARK 3 RMSD BOND DISTANCES 0.008 ANGSTROMS 1RBL 30 REMARK 3 RMSD BOND ANGLES 1.26 DEGREES 1RBL 31 REMARK 3 RMSD DIHEDRALS 26.12 DEGREES 1RBL 32 REMARK 3 RMSD IMPROPERS 1.26 DEGREES 1RBL 33 REMARK 3 1RBL 34 REMARK 3 NUMBER OF PROTEIN ATOMS 4562 1RBL 35 REMARK 3 NUMBER OF SOLVENT ATOMS 292 1RBL 36 REMARK 4 1RBL 37 REMARK 4 COORDINATES INCLUDE THE TWO CHAINS (A AND M), 1RBL 38 REMARK 4 THAT MAKE UP 1/8TH OF THE TOTAL RUBISCO HEXADECAMER. ALSO 1RBL 39 REMARK 4 INCLUDED ARE A MAGNESIUM ION, CAP (A TIGHT BINDING 1RBL 40 REMARK 4 SUBSTRATE ANALOGUE) AND 292 WATERS. THE MAKEUP OF THE 1RBL 41 REMARK 4 COMPLETE PROTEIN IS L8S8, WHERE L=LARGE AND S=SMALL 1RBL 42 REMARK 4 SUBUNITS. THE STRUCTURE IS REALLY A BUNDLE OF 4 LARGE 1RBL 43 REMARK 4 SUBUNIT DIMERS, ARRANGED AROUND A LOCAL FOUR-FOLD AXIS, AND 1RBL 44 REMARK 4 THIS IS CAPPED AT BOTH ENDS BY 4 S SUBUNITS (WHICH ALSO 1RBL 45 REMARK 4 OBEY THE LOCAL FOUR-FOLD). 1RBL 46 REMARK 5 1RBL 47 REMARK 5 THE CHAIN LABELING OF THE HEXADECAMERIC ENZYME IS AS 1RBL 48 REMARK 5 FOLLOWS: LARGE SUBUNITS ARE LABELLED A TO H, WITH 1RBL 49 REMARK 5 AB, CD, EF, GH AS THE CATALYTICALLY COMPETENT DIMERS. 1RBL 50 REMARK 5 SMALL SUBUNITS I, J, K, L ARE FOUND AT ONE END OF THE 1RBL 51 REMARK 5 HEXADECAMER, AND M, N, O, P ARE FOUND AT THE OTHER END. 1RBL 52 REMARK 6 1RBL 53 REMARK 6 SHEET LN1 IS -2X, +1, +2X. 1RBL 54 REMARK 7 1RBL 55 REMARK 7 THE DSSP RUN DID NOT INDICATE THAT STRAND 2 WAS INDEED A 1RBL 56 REMARK 7 STRAND. HOWEVER, THE A/B BARREL IS CLEARLY THAT, SO STRAND 1RBL 57 REMARK 7 2 IS INCLUDED AS A "REAL" STRAND. 1RBL 58 REMARK 8 1RBL 59 REMARK 8 HELICES A, B, BB, C, AND D PRESENTED ON THE HELIX RECORD 1RBL 60 REMARK 8 BELOW ARE THE HELICES OF THE N-TERMINAL DOMAIN. 1RBL 61 REMARK 9 1RBL 62 REMARK 9 SHEET SS1 IS +1,-2X,-1. 1RBL 63 REMARK 10 1RBL 64 REMARK 10 SITE CAB IS THE MAGNESIUM BINDING SITE, 1P IS THE BINDING 1RBL 65 REMARK 10 SITE OF THE FIRST PHOSPHATE GROUP OF THE CAP, 2P IS THE 1RBL 66 REMARK 10 BINDING SITE OF THE 2ND PHOSPHATE OF CAP, AND CAB ARE THE 1RBL 67 REMARK 10 OTHER RESIDUES INVOLVED IN BINDING THE CAP. NOTE THAT 1RBL 68 REMARK 10 RESIDUES OF LARGE SUBUNITS A AND B ARE NEEDED TO CREATE 1RBL 69 REMARK 10 THE CAP BINDING SITE. 1RBL 70 REMARK 11 1RBL 71 REMARK 11 THERE ARE SEVEN NON-CRYSTALLOGRAPHIC SYMMETRY OPERATORS, 1RBL 72 REMARK 11 AND THESE MUST BE USED TO GENERATE THE ENTIRE L8S8 1RBL 73 REMARK 11 MOLECULE. THE FORMAT OF THE FOLLOWING TRANSFORMATIONS IS 1RBL 74 REMARK 11 FROM X-PLOR, THUS THE SYMMETRY RELATED CHAINS ARE GENERATED 1RBL 75 REMARK 11 BY R'=R*R + T, R=ROTATION MATRIX, T=TRANSLATION. 1RBL 76 REMARK 12 1RBL 77 REMARK 12 THE SHEET PRESENTED AS *LC1* ON SHEET RECORDS BELOW IS 1RBL 78 REMARK 12 ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS 1RBL 79 REMARK 12 REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST 1RBL 80 REMARK 12 AND LAST STRANDS ARE IDENTICAL. 1RBL 81 REMARK 13 1RBL 82 REMARK 13 THESE ARE THE ROTATION/TRANSLATION COMPONENTS TO MAP AN 1RBL 83 REMARK 13 LS MONOMER (AM) ONTO THE REST OF THE MOLECULE. THESE 1RBL 84 REMARK 13 MATRICES WERE OBTAINED FROM X-PLOR AFTER REFINEMENT OF THE 1RBL 85 REMARK 13 WHOLE L8S8 920710. 1RBL 86 REMARK 13 1RBL 87 REMARK 13 MTRIX 1 TAKES AM TO BI. 1RBL 88 REMARK 13 1RBL 89 REMARK 13 MTRIX 2 TAKES AM TO CN. 1RBL 90 REMARK 13 1RBL 91 REMARK 13 MTRIX 3 TAKES AM TO DJ. 1RBL 92 REMARK 13 1RBL 93 REMARK 13 MTRIX 4 TAKES AM TO EO. 1RBL 94 REMARK 13 1RBL 95 REMARK 13 MTRIX 5 TAKES AM TO FK. 1RBL 96 REMARK 13 1RBL 97 REMARK 13 MTRIX 6 TAKES AM TO GP. 1RBL 98 REMARK 13 1RBL 99 REMARK 13 MTRIX 7 TAKES AM TO HL. 1RBL 100 REMARK 14 1RBL 101 REMARK 14 SEQUENCE ADVISORY NOTICE 1RBL 102 REMARK 14 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. 1RBL 103 REMARK 14 1RBL 104 REMARK 14 SWISS-PROT ENTRY NAME: RBL_SYNP6 1RBL 105 REMARK 14 1RBL 106 REMARK 14 SWISS-PROT RESIDUE PDB SEQRES 1RBL 107 REMARK 14 1RBL 108 REMARK 14 NAME NUMBER NAME CHAIN SEQ/INSERT CODE 1RBL 109 REMARK 14 PRO 38 ARG A 41 1RBL 110 REMARK 14 VAL 39 PHE A 42 1RBL 111 REMARK 14 GLN 88 ALA A 91 1RBL 112 REMARK 14 ARG 353 ALA A 356 1RBL 113 REMARK 14 ASP 64 ALA M 76 1RBL 114 REMARK 14 LYS 66 ALA M 78 1RBL 115 REMARK 14 SER 67 ALA M 79 1RBL 116 REMARK 14 GLN 97 GLU M 109 1RBL 117 REMARK 14 VAL 101 SER M 113 1RBL 118 REMARK 15 1RBL 119 REMARK 15 PDB ADVISORY NOTICE: 1RBL 120 REMARK 15 THE FOLLOWING CLOSE CONTACTS ARE OBSERVED: 1RBL 121 REMARK 15 158 A GLU OE2 325 A HIS NE2 SIDE-SIDE 2.4 1RBL 122 REMARK 15 350 A ARG NH2 394 A PHE O SIDE-MAIN 2.2 1RBL 123 REMARK 15 435 A ARG NH2 447 A GLU OE2 SIDE-SIDE 2.3 1RBL 124 REMARK 16 1RBL 125 REMARK 16 RESIDUES 9, 10, 11, 12 OF CHAIN *A* AND 122 OF CHAIN *M* 1RBL 126 REMARK 16 HAVE OCCUPANCY OF 0.0. 1RBL 127 REMARK 17 1RBLA 4 REMARK 17 CORRECTION. CORRECT TYPOGRAPHICAL ERROR IN AUTHOR AND JRNL 1RBLA 5 REMARK 17 RECORDS. 08-MAR-95. 1RBLA 6 SEQRES 1 A 467 SER ALA ALA GLY TYR LYS ALA GLY VAL LYS ASP TYR LYS 1RBL 128 SEQRES 2 A 467 LEU THR TYR TYR THR PRO ASP TYR THR PRO LYS ASP THR 1RBL 129 SEQRES 3 A 467 ASP LEU LEU ALA ALA PHE ARG PHE SER PRO GLN PRO GLY 1RBL 130 SEQRES 4 A 467 VAL PRO ALA ASP GLU ALA GLY ALA ALA ILE ALA ALA GLU 1RBL 131 SEQRES 5 A 467 SER SER THR GLY THR TRP THR THR VAL TRP THR ASP LEU 1RBL 132 SEQRES 6 A 467 LEU THR ASP MET ASP ARG TYR LYS GLY LYS CYS TYR HIS 1RBL 133 SEQRES 7 A 467 ILE GLU PRO VAL ALA GLY GLU GLU ASN SER TYR PHE ALA 1RBL 134 SEQRES 8 A 467 PHE ILE ALA TYR PRO LEU ASP LEU PHE GLU GLU GLY SER 1RBL 135 SEQRES 9 A 467 VAL THR ASN ILE LEU THR SER ILE VAL GLY ASN VAL PHE 1RBL 136 SEQRES 10 A 467 GLY PHE LYS ALA ILE ARG SER LEU ARG LEU GLU ASP ILE 1RBL 137 SEQRES 11 A 467 ARG PHE PRO VAL ALA LEU VAL LYS THR PHE GLN GLY PRO 1RBL 138 SEQRES 12 A 467 PRO HIS GLY ILE GLN VAL GLU ARG ASP LEU LEU ASN LYS 1RBL 139 SEQRES 13 A 467 TYR GLY ARG PRO MET LEU GLY CYS THR ILE LYS PRO LYS 1RBL 140 SEQRES 14 A 467 LEU GLY LEU SER ALA LYS ASN TYR GLY ARG ALA VAL TYR 1RBL 141 SEQRES 15 A 467 GLU CYS LEU ARG GLY GLY LEU ASP PHE THR LYS ASP ASP 1RBL 142 SEQRES 16 A 467 GLU ASN ILE ASN SER GLN PRO PHE GLN ARG TRP ARG ASP 1RBL 143 SEQRES 17 A 467 ARG PHE LEU PHE VAL ALA ASP ALA ILE HIS LYS SER GLN 1RBL 144 SEQRES 18 A 467 ALA GLU THR GLY GLU ILE LYS GLY HIS TYR LEU ASN VAL 1RBL 145 SEQRES 19 A 467 THR ALA PRO THR CYS GLU GLU MET MET LYS ARG ALA GLU 1RBL 146 SEQRES 20 A 467 PHE ALA LYS GLU LEU GLY MET PRO ILE ILE MET HIS ASP 1RBL 147 SEQRES 21 A 467 PHE LEU THR ALA GLY PHE THR ALA ASN THR THR LEU ALA 1RBL 148 SEQRES 22 A 467 LYS TRP CYS ARG ASP ASN GLY VAL LEU LEU HIS ILE HIS 1RBL 149 SEQRES 23 A 467 ARG ALA MET HIS ALA VAL ILE ASP ARG GLN ARG ASN HIS 1RBL 150 SEQRES 24 A 467 GLY ILE HIS PHE ARG VAL LEU ALA LYS CYS LEU ARG LEU 1RBL 151 SEQRES 25 A 467 SER GLY GLY ASP HIS LEU HIS SER GLY THR VAL VAL GLY 1RBL 152 SEQRES 26 A 467 LYS LEU GLU GLY ASP LYS ALA SER THR LEU GLY PHE VAL 1RBL 153 SEQRES 27 A 467 ASP LEU MET ARG GLU ASP HIS ILE GLU ALA ASP ARG SER 1RBL 154 SEQRES 28 A 467 ARG GLY VAL PHE PHE THR GLN ASP TRP ALA SER MET PRO 1RBL 155 SEQRES 29 A 467 GLY VAL LEU PRO VAL ALA SER GLY GLY ILE HIS VAL TRP 1RBL 156 SEQRES 30 A 467 HIS MET PRO ALA LEU VAL GLU ILE PHE GLY ASP ASP SER 1RBL 157 SEQRES 31 A 467 VAL LEU GLN PHE GLY GLY GLY THR LEU GLY HIS PRO TRP 1RBL 158 SEQRES 32 A 467 GLY ASN ALA PRO GLY ALA THR ALA ASN ARG VAL ALA LEU 1RBL 159 SEQRES 33 A 467 GLU ALA CYS VAL GLN ALA ARG ASN GLU GLY ARG ASP LEU 1RBL 160 SEQRES 34 A 467 TYR ARG GLU GLY GLY ASP ILE LEU ARG GLU ALA GLY LYS 1RBL 161 SEQRES 35 A 467 TRP SER PRO GLU LEU ALA ALA ALA LEU ASP LEU TRP LYS 1RBL 162 SEQRES 36 A 467 GLU ILE LYS PHE GLU PHE GLU THR MET ASP LYS LEU 1RBL 163 SEQRES 1 M 109 SER MET LYS THR LEU PRO LYS GLU ARG ARG PHE GLU THR 1RBL 164 SEQRES 2 M 109 PHE SER TYR LEU PRO PRO LEU SER ASP ARG GLN ILE ALA 1RBL 165 SEQRES 3 M 109 ALA GLN ILE GLU TYR MET ILE GLU GLN GLY PHE HIS PRO 1RBL 166 SEQRES 4 M 109 LEU ILE GLU PHE ASN GLU HIS SER ASN PRO GLU GLU PHE 1RBL 167 SEQRES 5 M 109 TYR TRP THR MET TRP LYS LEU PRO LEU PHE ALA CYS ALA 1RBL 168 SEQRES 6 M 109 ALA PRO GLN GLN VAL LEU ASP GLU VAL ARG GLU CYS ARG 1RBL 169 SEQRES 7 M 109 SER GLU TYR GLY ASP CYS TYR ILE ARG VAL ALA GLY PHE 1RBL 170 SEQRES 8 M 109 ASP ASN ILE LYS GLU CYS GLN THR SER SER PHE ILE VAL 1RBL 171 SEQRES 9 M 109 HIS ARG PRO GLY ARG 1RBL 172 FTNOTE 1 1RBL 173 FTNOTE 1 CIS PROLINE - PRO A 176 1RBL 174 HET CAP 476 21 2-CARBOXYARABINITOL 1,5 BIPHOSHPATE 1RBL 175 HET CBX A 201 3 CARBOXYLIC GROUP 1RBL 176 HET MG 477 1 MAGNESIUM ++ 1RBL 177 FORMUL 3 CAP C6 H9 O13 P2 1RBL 178 FORMUL 4 CBX C1 H1 O2 1RBL 179 FORMUL 5 MG MG1 ++ 1RBL 180 FORMUL 6 HOH *292(H2 O1) 1RBL 181 HELIX 1 A LYS A 21 TYR A 24 1 SEE REMARK 8. 1RBL 182 HELIX 2 B ALA A 50 GLU A 60 1 SEE REMARK 8. 1RBL 183 HELIX 3 BB MET A 77 TYR A 80 1 SEE REMARK 8. 1RBL 184 HELIX 4 C VAL A 113 VAL A 121 1 SEE REMARK 8. 1RBL 185 HELIX 5 D VAL A 142 VAL A 145 1 SEE REMARK 8. 1RBL 186 HELIX 6 E ILE A 155 LEU A 162 1 LINKS N-TERM & C-TERM DOMAINS 1RBL 187 HELIX 7 1 ALA A 182 ARG A 194 1 FIRST HELIX OF A/B BARREL 1RBL 188 HELIX 8 2 TRP A 214 THR A 232 1 2ND HELIX OF A/B BARREL 1RBL 189 HELIX 9 3 CYS A 247 GLU A 259 1 3RD HELIX OF A/B BARREL 1RBL 190 HELIX 10 4 PHE A 269 ASN A 287 1 4TH HELIX OF A/B BARREL 1RBL 191 HELIX 11 F HIS A 298 ASP A 302 1 1RBL 192 HELIX 12 5 PHE A 311 SER A 321 1 5TH HELIX OF A/B BARREL 1RBL 193 HELIX 13 6 LYS A 339 ARG A 350 1 6TH HELIX OF A/B BARREL 1RBL 194 HELIX 14 7 MET A 387 PHE A 394 1 7TH HELIX OF A/B BARREL 1RBL 195 HELIX 15 P GLY A 404 LEU A 407 1 P FOR PHOSPHATE BINDING HELIX 1RBL 196 HELIX 16 8 ASN A 413 GLU A 433 1 8TH HELIX OF A/B BARREL 1RBL 197 HELIX 17 G LEU A 437 TRP A 451 1 1RBL 198 HELIX 18 H PRO A 453 TRP A 462 1 1RBL 199 HELIX 19 A' THR A 23 GLN M 36 1 1ST HELIX - SMALL SUBUNIT 1RBL 200 HELIX 20 B' TYR A 80 GLU M 93 1 2ND HELIX - SMALL SUBUNIT 1RBL 201 SHEET 1 LN1 4 LYS A 83 PRO A 89 0 1RBL 202 SHEET 2 LN1 4 SER A 96 TYR A 103 -1 1RBL 203 SHEET 3 LN1 4 LEU A 36 PRO A 44 -1 1RBL 204 SHEET 4 LN1 4 ILE A 130 ARG A 139 -1 1RBL 205 SHEET 1 LC1 9 MET A 169 GLY A 171 0 1RBL 206 SHEET 2 LC1 9 THR A 200 ASP A 202 1 1RBL 207 SHEET 3 LC1 9 LEU A 240 ASN A 241 1 1RBL 208 SHEET 4 LC1 9 ILE A 264 ASP A 268 1 1RBL 209 SHEET 5 LC1 9 LEU A 290 HIS A 294 1 1RBL 210 SHEET 6 LC1 9 HIS A 325 HIS A 327 1 1RBL 211 SHEET 7 LC1 9 LEU A 375 SER A 379 1 1RBL 212 SHEET 8 LC1 9 VAL A 399 GLN A 401 1 1RBL 213 SHEET 9 LC1 9 MET A 169 GLY A 171 1 1RBL 214 SHEET 1 SS1 4 THR M 68 MET M 69 0 1RBL 215 SHEET 2 SS1 4 HIS M 39 ASN M 45 -1 1RBL 216 SHEET 3 SS1 4 TYR M 98 ASP M 105 -1 1RBL 217 SHEET 4 SS1 4 CYS M 110 HIS M 118 -1 1RBL 218 SITE 1 MG 3 LYS A 201 ASP A 203 GLU A 204 1RBL 219 SITE 1 1P 4 PHE M 65 GLY A 404 GLY A 381 GLY A 403 1RBL 220 SITE 1 2P 2 ARG A 295 HIS A 327 1RBL 221 SITE 1 CAB 6 MG 477 THR B 173 LYS B 175 LYS A 201 1RBL 222 SITE 2 CAB 6 HIS A 294 SER A 379 1RBL 223 CRYST1 223.900 111.900 199.700 90.00 90.00 90.00 P 21 21 21 4 1RBL 224 ORIGX1 1.000000 0.000000 0.000000 0.00000 1RBL 225 ORIGX2 0.000000 1.000000 0.000000 0.00000 1RBL 226 ORIGX3 0.000000 0.000000 1.000000 0.00000 1RBL 227 SCALE1 0.004466 0.000000 0.000000 0.00000 1RBL 228 SCALE2 0.000000 0.008937 0.000000 0.00000 1RBL 229 SCALE3 0.000000 0.000000 0.005008 0.00000 1RBL 230 MTRIX1 1 0.055254 0.991591 0.117024 58.51700 1RBL 231 MTRIX2 1 0.991747 -0.068084 0.108639 -60.77910 1RBL 232 MTRIX3 1 0.115693 0.110056 -0.987169 -12.31830 1RBL 233 MTRIX1 2 -0.001556 0.994481 0.104910 63.24410 1RBL 234 MTRIX2 2 -0.993326 0.010562 -0.114852 104.72470 1RBL 235 MTRIX3 2 -0.115326 -0.104388 0.987827 11.96200 1RBL 236 MTRIX1 3 0.998390 -0.056422 0.005795 1.35870 1RBL 237 MTRIX2 3 -0.056413 -0.998406 -0.001652 47.27970 1RBL 238 MTRIX3 3 0.005879 0.001323 -0.999982 -0.77360 1RBL 239 MTRIX1 4 -0.999944 0.000591 -0.010574 168.35741 1RBL 240 MTRIX2 4 0.001717 -0.976187 -0.216926 41.89850 1RBL 241 MTRIX3 4 -0.010451 -0.216932 0.976131 5.47850 1RBL 242 MTRIX1 5 -0.055113 -0.992904 -0.105381 109.87600 1RBL 243 MTRIX2 5 -0.993265 0.043745 0.107292 104.02560 1RBL 244 MTRIX3 5 -0.101920 0.110584 -0.988627 5.96800 1RBL 245 MTRIX1 6 -0.000233 -0.993280 -0.115738 105.29090 1RBL 246 MTRIX2 6 0.994670 0.011703 -0.102440 -62.72860 1RBL 247 MTRIX3 6 0.103106 -0.115145 0.987983 -6.23160 1RBL 248 MTRIX1 7 -0.998513 0.054364 0.004006 167.12070 1RBL 249 MTRIX2 7 0.053928 0.974438 0.218086 -3.88990 1RBL 250 MTRIX3 7 0.007953 0.217978 -0.975921 -5.57330 1RBL 251