HEADER TRANSFERASE(GLUCANOTRANSFERASE) 02-AUG-93 1CDG 1CDG 2 COMPND CYCLODEXTRIN GLYCOSYLTRANSFERASE (E.C.2.4.1.19) (CGTASE) 1CDG 3 SOURCE (BACILLUS CIRCULANS, STRAIN 251) 1CDG 4 AUTHOR C.L.LAWSON,R.VAN MONTFORT,B.V.STROKOPYTOV,K.H.KALK, 1CDG 5 AUTHOR 2 H.J.ROZEBOOM,B.W.DIJKSTRA 1CDG 6 REVDAT 2 08-MAR-95 1CDGA 1 JRNL REMARK 1CDGA 1 REVDAT 1 31-JAN-94 1CDG 0 1CDG 7 JRNL AUTH C.L.LAWSON,R.VAN MONTFORT,B.STROKOPYTOV, 1CDG 8 JRNL AUTH 2 H.J.ROZEBOOM,K.H.KALK,G.E.DE VRIES,D.PENNINGA, 1CDG 9 JRNL AUTH 3 L.DIJKHUIZEN,B.W.DIJKSTRA 1CDG 10 JRNL TITL NUCLEOTIDE SEQUENCE AND X-RAY STRUCTURE OF 1CDG 11 JRNL TITL 2 CYCLODEXTRIN GLYCOSYLTRANSFERASE FROM BACILLUS 1CDG 12 JRNL TITL 3 CIRCULANS STRAIN 251 IN A MALTOSE-DEPENDENT 1CDG 13 JRNL TITL 4 CRYSTAL FORM 1CDG 14 JRNL REF J.MOL.BIOL. V. 236 590 1994 1CDGA 2 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 0070 1CDGA 3 REMARK 1 1CDG 17 REMARK 1 REFERENCE 1 1CDG 18 REMARK 1 AUTH C.L.LAWSON,J.BERGSMA,P.M.BRUINENBERG,G.DE VRIES, 1CDG 19 REMARK 1 AUTH 2 L.DIJKHUIZEN,B.W.DIJKSTRA 1CDG 20 REMARK 1 TITL MALTODEXTRIN-DEPENDENT CRYSTALLIZATION OF 1CDG 21 REMARK 1 TITL 2 CYCLOMALTODEXTRIN GLUCANOTRANSFERASE FROM 1CDG 22 REMARK 1 TITL 3 BACILLUS CIRCULANS 1CDG 23 REMARK 1 REF J.MOL.BIOL. V. 214 807 1990 1CDG 24 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 0070 1CDGA 4 REMARK 2 1CDG 26 REMARK 2 RESOLUTION. 2.0 ANGSTROMS. 1CDG 27 REMARK 3 1CDG 28 REMARK 3 REFINEMENT. 1CDG 29 REMARK 3 PROGRAM TNT 1CDG 30 REMARK 3 AUTHORS TRONRUD,TEN EYCK,MATTHEWS 1CDG 31 REMARK 3 R VALUE 0.164 1CDG 32 REMARK 3 RMSD BOND DISTANCES 0.016 ANGSTROMS 1CDG 33 REMARK 3 RMSD BOND ANGLES 2.46 DEGREES 1CDG 34 REMARK 3 DATA CUTOFF 0.0 SIGMA(F) 1CDG 35 REMARK 3 1CDG 36 REMARK 3 NUMBER OF PROTEIN ATOMS 5264 1CDG 37 REMARK 3 NUMBER OF SOLVENT ATOMS 471 1CDG 38 REMARK 3 1CDG 39 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF 1CDG 40 REMARK 3 SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED 1CDG 41 REMARK 3 STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE 1CDG 42 REMARK 3 WEIGHTS OF THE CORRESPONDING RESTRAINTS) 1CDG 43 REMARK 3 DISTANCE RESTRAINTS (ANGSTROMS) 1CDG 44 REMARK 3 BOND DISTANCE 0.016(0.020) 1CDG 45 REMARK 3 ANGLE DISTANCE (DEGREES) 2.460(3.000) 1CDG 46 REMARK 3 PLANAR GROUPS RESTRAINT 0.018(0.020) 1CDG 47 REMARK 3 TRIGONAL ATOM PLANARITY 0.015(0.020) 1CDG 48 REMARK 3 NON-BONDED CONTACT RESTRAINTS 1CDG 49 REMARK 3 MULTIPLE TORSION CONTACT 0.029(0.100) 1CDG 50 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINT 1CDG 51 REMARK 3 (DEGREES) 24.670(30.00) 1CDG 52 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS (ANGSTROMS**2) 1CDG 53 REMARK 3 MAIN-CHAIN BOND 2.170(2.230) 1CDG 54 REMARK 3 SIDE-CHAIN BOND 2.170(2.230) 1CDG 55 REMARK 3 1CDG 56 REMARK 3 NOTE: 1CDG 57 REMARK 3 1CDG 58 REMARK 3 THE WEIGHTING SCHEME IN TNT DIFFERS FROM 1CDG 59 REMARK 3 THAT DEFINED IN HENDRICKSON-KONNERT PROGRAM. IN ORDER 1CDG 60 REMARK 3 TO GET REAL WEIGHTS, WEIGHTS DEFINED AS (1.0/SIGMA**2) 1CDG 61 REMARK 3 WERE MULTIPLIED BY A CORRESPONDING FACTOR TAKEN FROM 1CDG 62 REMARK 3 TABLE BELOW. 1CDG 63 REMARK 3 1CDG 64 REMARK 3 TABLE: ADDITIONAL WEIGHTING FACTORS FOR 1CDG 65 REMARK 3 DIFFERENT CLASSES OF RESTRAINTS 1CDG 66 REMARK 3 USED DURING REFINEMENT. 1CDG 67 REMARK 3 1CDG 68 REMARK 3 FACTOR 1CDG 69 REMARK 3 BOND LENGTHS 3.0 1CDG 70 REMARK 3 BOND ANGLES 5.5 1CDG 71 REMARK 3 TORSION ANGLES 0.0 1CDG 72 REMARK 3 TRIGONAL ATOM PLANARITY 5.0 1CDG 73 REMARK 3 PLANAR GROUPS 15.0 1CDG 74 REMARK 3 NON-BONDED CONTACTS 20.0 1CDG 75 REMARK 3 RMS B-VALUES DEVIATION BETWEEN 1.000 1CDG 76 REMARK 3 BONDED ATOMS 1CDG 77 REMARK 4 1CDG 78 REMARK 4 ABBREVIATIONS USED: 1CDG 79 REMARK 4 1CDG 80 REMARK 4 CAT = CATALYTIC RESIDUE SITE 1CDG 81 REMARK 4 CA1 = 1ST CALCIUM ION BINDING SITE 1CDG 82 REMARK 4 CA2 = 2ND CALCIUM ION BINDING SITE 1CDG 83 REMARK 4 MB1 = 1ST MALTOSE BINDING SITE (MAL 689) 1CDG 84 REMARK 4 MB2 = 2ND MALTOSE BINDING SITE (MAL 690) 1CDG 85 REMARK 4 MB3 = 3RD MALTOSE BINDING SITE (MAL 688) 1CDG 86 REMARK 5 1CDG 87 REMARK 5 RESIDUES 54 - 62 AND 65 - 68 OF THE HELIX RECORD BELOW 1CDG 88 REMARK 5 CONSTITUTE ONE HELIX. 1CDG 89 REMARK 6 1CDG 90 REMARK 6 THE SHEET PRESENTED AS *AB8* ON SHEET RECORDS BELOW IS 1CDG 91 REMARK 6 ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS 1CDG 92 REMARK 6 REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST 1CDG 93 REMARK 6 AND LAST STRANDS ARE IDENTICAL. 1CDG 94 REMARK 7 1CDG 95 REMARK 7 SITE MB1 INCLUDES RESIDUE SER 382 FOR SYMMETRY-RELATED 1CDG 96 REMARK 7 MOLECULE. SITE MB3 INCLUDES THE FOLLOWING RESIDUES FOR 1CDG 97 REMARK 7 SYMMETRY RELATED MOLECULE: SER 537, ALA 539, ASP 540. 1CDG 98 REMARK 8 1CDG 99 REMARK 8 THE STRUCTURE CONSISTS OF 5 DOMAINS: 1CDG 100 REMARK 8 1CDG 101 REMARK 8 DOMAIN RESIDUES COMMENT 1CDG 102 REMARK 8 1CDG 103 REMARK 8 A 1 - 143 (BETA-ALPHA) 8 TOPOLOGY (TIM 1CDG 104 REMARK 8 A 205 - 406 BARREL) 1CDG 105 REMARK 8 B 144 - 204 1CDG 106 REMARK 8 C 407 - 495 1CDG 107 REMARK 8 D 496 - 583 1CDG 108 REMARK 8 E 584 - 686 1CDG 109 REMARK 9 1CDG 110 REMARK 9 THERE IS ONE DISTANT WATER (146). 1CDG 111 REMARK 10 1CDGA 5 REMARK 10 CORRECTION. UPDATE JRNL REFERENCE TO REFLECT PUBLICATION. 1CDGA 6 REMARK 10 REVISE CODEN FOR REFERENCE 1. 08-MAR-95. 1CDGA 7 SEQRES 1 686 ALA PRO ASP THR SER VAL SER ASN LYS GLN ASN PHE SER 1CDG 112 SEQRES 2 686 THR ASP VAL ILE TYR GLN ILE PHE THR ASP ARG PHE SER 1CDG 113 SEQRES 3 686 ASP GLY ASN PRO ALA ASN ASN PRO THR GLY ALA ALA PHE 1CDG 114 SEQRES 4 686 ASP GLY THR CYS THR ASN LEU ARG LEU TYR CYS GLY GLY 1CDG 115 SEQRES 5 686 ASP TRP GLN GLY ILE ILE ASN LYS ILE ASN ASP GLY TYR 1CDG 116 SEQRES 6 686 LEU THR GLY MET GLY VAL THR ALA ILE TRP ILE SER GLN 1CDG 117 SEQRES 7 686 PRO VAL GLU ASN ILE TYR SER ILE ILE ASN TYR SER GLY 1CDG 118 SEQRES 8 686 VAL ASN ASN THR ALA TYR HIS GLY TYR TRP ALA ARG ASP 1CDG 119 SEQRES 9 686 PHE LYS LYS THR ASN PRO ALA TYR GLY THR ILE ALA ASP 1CDG 120 SEQRES 10 686 PHE GLN ASN LEU ILE ALA ALA ALA HIS ALA LYS ASN ILE 1CDG 121 SEQRES 11 686 LYS VAL ILE ILE ASP PHE ALA PRO ASN HIS THR SER PRO 1CDG 122 SEQRES 12 686 ALA SER SER ASP GLN PRO SER PHE ALA GLU ASN GLY ARG 1CDG 123 SEQRES 13 686 LEU TYR ASP ASN GLY THR LEU LEU GLY GLY TYR THR ASN 1CDG 124 SEQRES 14 686 ASP THR GLN ASN LEU PHE HIS HIS ASN GLY GLY THR ASP 1CDG 125 SEQRES 15 686 PHE SER THR THR GLU ASN GLY ILE TYR LYS ASN LEU TYR 1CDG 126 SEQRES 16 686 ASP LEU ALA ASP LEU ASN HIS ASN ASN SER THR VAL ASP 1CDG 127 SEQRES 17 686 VAL TYR LEU LYS ASP ALA ILE LYS MET TRP LEU ASP LEU 1CDG 128 SEQRES 18 686 GLY ILE ASP GLY ILE ARG MET ASP ALA VAL LYS HIS MET 1CDG 129 SEQRES 19 686 PRO PHE GLY TRP GLN LYS SER PHE MET ALA ALA VAL ASN 1CDG 130 SEQRES 20 686 ASN TYR LYS PRO VAL PHE THR PHE GLY GLU TRP PHE LEU 1CDG 131 SEQRES 21 686 GLY VAL ASN GLU VAL SER PRO GLU ASN HIS LYS PHE ALA 1CDG 132 SEQRES 22 686 ASN GLU SER GLY MET SER LEU LEU ASP PHE ARG PHE ALA 1CDG 133 SEQRES 23 686 GLN LYS VAL ARG GLN VAL PHE ARG ASP ASN THR ASP ASN 1CDG 134 SEQRES 24 686 MET TYR GLY LEU LYS ALA MET LEU GLU GLY SER ALA ALA 1CDG 135 SEQRES 25 686 ASP TYR ALA GLN VAL ASP ASP GLN VAL THR PHE ILE ASP 1CDG 136 SEQRES 26 686 ASN HIS ASP MET GLU ARG PHE HIS ALA SER ASN ALA ASN 1CDG 137 SEQRES 27 686 ARG ARG LYS LEU GLU GLN ALA LEU ALA PHE THR LEU THR 1CDG 138 SEQRES 28 686 SER ARG GLY VAL PRO ALA ILE TYR TYR GLY THR GLU GLN 1CDG 139 SEQRES 29 686 TYR MET SER GLY GLY THR ASP PRO ASP ASN ARG ALA ARG 1CDG 140 SEQRES 30 686 ILE PRO SER PHE SER THR SER THR THR ALA TYR GLN VAL 1CDG 141 SEQRES 31 686 ILE GLN LYS LEU ALA PRO LEU ARG LYS CYS ASN PRO ALA 1CDG 142 SEQRES 32 686 ILE ALA TYR GLY SER THR GLN GLU ARG TRP ILE ASN ASN 1CDG 143 SEQRES 33 686 ASP VAL LEU ILE TYR GLU ARG LYS PHE GLY SER ASN VAL 1CDG 144 SEQRES 34 686 ALA VAL VAL ALA VAL ASN ARG ASN LEU ASN ALA PRO ALA 1CDG 145 SEQRES 35 686 SER ILE SER GLY LEU VAL THR SER LEU PRO GLN GLY SER 1CDG 146 SEQRES 36 686 TYR ASN ASP VAL LEU GLY GLY LEU LEU ASN GLY ASN THR 1CDG 147 SEQRES 37 686 LEU SER VAL GLY SER GLY GLY ALA ALA SER ASN PHE THR 1CDG 148 SEQRES 38 686 LEU ALA ALA GLY GLY THR ALA VAL TRP GLN TYR THR ALA 1CDG 149 SEQRES 39 686 ALA THR ALA THR PRO THR ILE GLY HIS VAL GLY PRO MET 1CDG 150 SEQRES 40 686 MET ALA LYS PRO GLY VAL THR ILE THR ILE ASP GLY ARG 1CDG 151 SEQRES 41 686 GLY PHE GLY SER SER LYS GLY THR VAL TYR PHE GLY THR 1CDG 152 SEQRES 42 686 THR ALA VAL SER GLY ALA ASP ILE THR SER TRP GLU ASP 1CDG 153 SEQRES 43 686 THR GLN ILE LYS VAL LYS ILE PRO ALA VAL ALA GLY GLY 1CDG 154 SEQRES 44 686 ASN TYR ASN ILE LYS VAL ALA ASN ALA ALA GLY THR ALA 1CDG 155 SEQRES 45 686 SER ASN VAL TYR ASP ASN PHE GLU VAL LEU SER GLY ASP 1CDG 156 SEQRES 46 686 GLN VAL SER VAL ARG PHE VAL VAL ASN ASN ALA THR THR 1CDG 157 SEQRES 47 686 ALA LEU GLY GLN ASN VAL TYR LEU THR GLY SER VAL SER 1CDG 158 SEQRES 48 686 GLU LEU GLY ASN TRP ASP PRO ALA LYS ALA ILE GLY PRO 1CDG 159 SEQRES 49 686 MET TYR ASN GLN VAL VAL TYR GLN TYR PRO ASN TRP TYR 1CDG 160 SEQRES 50 686 TYR ASP VAL SER VAL PRO ALA GLY LYS THR ILE GLU PHE 1CDG 161 SEQRES 51 686 LYS PHE LEU LYS LYS GLN GLY SER THR VAL THR TRP GLU 1CDG 162 SEQRES 52 686 GLY GLY SER ASN HIS THR PHE THR ALA PRO SER SER GLY 1CDG 163 SEQRES 53 686 THR ALA THR ILE ASN VAL ASN TRP GLN PRO 1CDG 164 FTNOTE 1 1CDG 165 FTNOTE 1 RESIDUES PRO 372, PRO 506, PRO 624, AND PRO 634 ARE CIS 1CDG 166 FTNOTE 1 PROLINES. 1CDG 167 HET MAL 688 23 MALTOSE 1CDG 168 HET MAL 689 23 MALTOSE 1CDG 169 HET MAL 690 23 MALTOSE 1CDG 170 HET CA 691 1 CALCIUM +2 COUNTER ION 1CDG 171 HET CA 692 1 CALCIUM +2 COUNTER ION 1CDG 172 FORMUL 2 MAL 3(C12 H22 O11) 1CDG 173 FORMUL 3 CA 2(CA1) 1CDG 174 FORMUL 4 HOH *471(H2 O1) 1CDG 175 HELIX 1 A1 TRP 54 ASN 62 1 1CDG 176 HELIX 2 A1' TYR 65 GLY 68 1 1CDG 177 HELIX 3 A2 ILE 115 ALA 127 1 1CDG 178 HELIX 4 A3 THR 185 LYS 192 1 1CDG 179 HELIX 5 A4 ASN 204 LEU 221 1 1CDG 180 HELIX 6 A5 PHE 236 ASN 248 1 1CDG 181 HELIX 7 A6 PRO 267 GLU 275 1 1CDG 182 HELIX 8 A7 PHE 283 PHE 293 1 1CDG 183 HELIX 9 A8 MET 300 ASP 313 1 1CDG 184 HELIX 10 A9 ARG 339 THR 351 1 1CDG 185 HELIX 11 A10 THR 385 CYS 400 1 1CDG 186 HELIX 12 A11 PRO 402 TYR 406 1 1CDG 187 SHEET 1 AB8 9 VAL 16 ILE 20 0 1CDG 188 SHEET 2 AB8 9 THR 72 ILE 76 1 N THR 72 O VAL 16 1CDG 189 SHEET 3 AB8 9 ILE 130 ALA 137 1 N LYS 131 O THR 72 1CDG 190 SHEET 4 AB8 9 GLY 225 ASP 229 1 O GLY 225 N ILE 134 1CDG 191 SHEET 5 AB8 9 PHE 253 GLU 257 1 O PHE 253 N ILE 226 1CDG 192 SHEET 6 AB8 9 SER 279 LEU 281 1 N SER 279 O THR 254 1CDG 193 SHEET 7 AB8 9 GLN 320 THR 322 1 N VAL 321 O LEU 280 1CDG 194 SHEET 8 AB8 9 VAL 355 TYR 359 1 N VAL 355 O GLN 320 1CDG 195 SHEET 9 AB8 9 VAL 16 ILE 20 1 N ILE 17 O PRO 356 1CDG 196 SHEET 1 B2 2 ILE 87 TYR 89 0 1CDG 197 SHEET 2 B2 2 VAL 92 ASN 94 -1 O ASN 94 N ILE 87 1CDG 198 SHEET 1 C4 4 PRO 79 ILE 83 0 1CDG 199 SHEET 2 C4 4 TRP 101 ASN 109 -1 O TRP 101 N ILE 83 1CDG 200 SHEET 3 C4 4 ARG 156 ASP 159 -1 N TYR 158 O ARG 103 1CDG 201 SHEET 4 C4 4 THR 162 GLY 165 -1 O THR 162 N ASP 159 1CDG 202 SHEET 1 E2 2 HIS 140 ALA 144 0 1CDG 203 SHEET 2 E2 2 LEU 197 LEU 200 -1 O ALA 198 N THR 141 1CDG 204 SHEET 1 I4 4 GLY 407 ASN 415 0 1CDG 205 SHEET 2 I4 4 ASP 417 PHE 425 -1 O VAL 418 N ASN 415 1CDG 206 SHEET 3 I4 4 SER 427 ARG 436 -1 N ASN 428 O PHE 425 1CDG 207 SHEET 4 I4 4 GLY 486 ALA 494 -1 O GLY 486 N ASN 435 1CDG 208 SHEET 1 J2 2 ALA 442 SER 445 0 1CDG 209 SHEET 2 J2 2 PHE 480 ALA 483 -1 N LEU 482 O ALA 442 1CDG 210 SHEET 1 M4 4 THR 500 GLY 505 0 1CDG 211 SHEET 2 M4 4 VAL 513 ARG 520 -1 N ARG 520 O THR 500 1CDG 212 SHEET 3 M4 4 THR 547 ILE 553 -1 N ILE 553 O VAL 513 1CDG 213 SHEET 4 M4 4 ILE 541 GLU 545 -1 N SER 543 O LYS 550 1CDG 214 SHEET 1 N5 5 MET 507 LYS 510 0 1CDG 215 SHEET 2 N5 5 VAL 575 LEU 582 1 N GLU 580 O MET 507 1CDG 216 SHEET 3 N5 5 GLY 559 ASN 567 -1 O ILE 563 N TYR 576 1CDG 217 SHEET 4 N5 5 THR 528 PHE 531 1 O THR 528 N ALA 566 1CDG 218 SHEET 5 N5 5 THR 534 SER 537 -1 O THR 534 N PHE 531 1CDG 219 SHEET 1 O3 3 ALA 678 TRP 684 0 1CDG 220 SHEET 2 O3 3 ASP 585 VAL 593 1 N ARG 590 O ALA 678 1CDG 221 SHEET 3 O3 3 ASN 635 PRO 643 -1 O VAL 642 N VAL 587 1CDG 222 SHEET 1 P3A 3 GLN 602 SER 609 0 1CDG 223 SHEET 2 P3A 3 LYS 646 GLN 656 -1 O LYS 655 N ASN 603 1CDG 224 SHEET 3 P3A 3 THR 659 GLU 663 -1 O THR 659 N GLN 656 1CDG 225 SHEET 1 P3B 3 GLN 602 SER 609 0 1CDG 226 SHEET 2 P3B 3 LYS 646 GLN 656 -1 O LYS 655 N ASN 603 1CDG 227 SHEET 3 P3B 3 HIS 668 ALA 672 -1 N HIS 668 O PHE 650 1CDG 228 SSBOND 1 CYS 43 CYS 50 1CDG 229 SITE 1 CAT 3 ASP 229 GLU 257 ASP 328 1CDG 230 SITE 1 CA1 6 ASP 27 ASN 29 ASN 32 ASN 33 1CDG 231 SITE 2 CA1 6 GLY 51 ASP 53 1CDG 232 SITE 1 CA2 4 ASN 139 ILE 190 ASP 199 HIS 233 1CDG 233 SITE 1 MB1 5 TRP 616 LYS 651 TRP 662 GLU 663 1CDG 234 SITE 2 MB1 5 ASN 667 1CDG 235 SITE 1 MB2 7 THR 598 ALA 599 GLY 601 ASN 603 1CDG 236 SITE 2 MB2 7 ASN 627 GLN 628 TYR 633 1CDG 237 SITE 1 MB3 7 TYR 301 GLU 411 ARG 412 TRP 413 1CDG 238 SITE 2 MB3 7 ILE 414 GLY 446 VAL 448 1CDG 239 CRYST1 120.363 110.935 66.429 90.00 90.00 90.00 P 21 21 21 4 1CDG 240 ORIGX1 1.000000 0.000000 0.000000 0.00000 1CDG 241 ORIGX2 0.000000 1.000000 0.000000 0.00000 1CDG 242 ORIGX3 0.000000 0.000000 1.000000 0.00000 1CDG 243 SCALE1 0.008308 0.000000 0.000000 0.00000 1CDG 244 SCALE2 0.000000 0.009014 0.000000 0.00000 1CDG 245 SCALE3 0.000000 0.000000 0.015054 0.00000 1CDG 246