HEADER TOXIN 23-MAY-18 6DIK TITLE CRYSTAL STRUCTURE OF BOTHROPSTOXIN I (BTHTX-I) COMPLEXED TO CHICORIC TITLE 2 ACID CAVEAT 6DIK FOR RESIDUES LYS A 53 AND LYS A 57 DISTANCE BETWEEN C AND N CAVEAT 2 6DIK ATOMS IS 1.06A COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC PHOSPHOLIPASE A2 HOMOLOG BOTHROPSTOXIN-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SVPLA2 HOMOLOG,BOJU-I,BOTHROPSTOXIN I,BTXTXI,MYOTOXIC COMPND 5 PHOSPHOLIPASE A2-LIKE,PHOSPHOLIPASE A2 HOMOLOG 1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOTHROPS JARARACUSSU; SOURCE 3 ORGANISM_COMMON: JARARACUSSU; SOURCE 4 ORGANISM_TAXID: 8726; SOURCE 5 TISSUE: VENOM GLANDS KEYWDS BOTHROPD JARARACUSSU, BTHTX-I, INHIBITOR, CHICORIC ACID, CICHORIC KEYWDS 2 ACID, PLA2, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR F.F.CARDOSO,G.H.M.SALVADOR,R.J.BORGES REVDAT 4 11-OCT-23 6DIK 1 REMARK REVDAT 3 01-JAN-20 6DIK 1 REMARK REVDAT 2 31-OCT-18 6DIK 1 JRNL REVDAT 1 03-OCT-18 6DIK 0 JRNL AUTH F.F.CARDOSO,R.J.BORGES,T.R.DREYER,G.H.M.SALVADOR, JRNL AUTH 2 W.L.G.CAVALCANTE,M.D.PAI,M.GALLACCI,M.R.M.FONTES JRNL TITL STRUCTURAL BASIS OF PHOSPHOLIPASE A2-LIKE MYOTOXIN JRNL TITL 2 INHIBITION BY CHICORIC ACID, A NOVEL POTENT INHIBITOR OF JRNL TITL 3 OPHIDIAN TOXINS. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1862 2728 2018 JRNL REF 2 SUBJ JRNL REFN ISSN 1872-8006 JRNL PMID 30251662 JRNL DOI 10.1016/J.BBAGEN.2018.08.002 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 17595 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 884 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.3490 - 3.4876 0.94 2723 140 0.1506 0.1641 REMARK 3 2 3.4876 - 2.7690 0.96 2760 148 0.1698 0.1915 REMARK 3 3 2.7690 - 2.4193 0.99 2813 149 0.1797 0.2683 REMARK 3 4 2.4193 - 2.1982 0.99 2827 150 0.1668 0.2302 REMARK 3 5 2.1982 - 2.0407 1.00 2855 149 0.1662 0.2166 REMARK 3 6 2.0407 - 1.9204 0.96 2733 148 0.1882 0.2347 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1997 REMARK 3 ANGLE : 0.694 2695 REMARK 3 CHIRALITY : 0.044 267 REMARK 3 PLANARITY : 0.004 342 REMARK 3 DIHEDRAL : 16.169 1234 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 19 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6808 -10.5140 9.8614 REMARK 3 T TENSOR REMARK 3 T11: 0.2661 T22: 0.2180 REMARK 3 T33: 0.1902 T12: 0.0582 REMARK 3 T13: -0.0177 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 8.1259 L22: 5.5649 REMARK 3 L33: 4.7159 L12: 1.9519 REMARK 3 L13: -1.9421 L23: -1.0877 REMARK 3 S TENSOR REMARK 3 S11: 0.1305 S12: 0.3426 S13: -0.4901 REMARK 3 S21: -0.1782 S22: -0.0188 S23: -0.0128 REMARK 3 S31: 0.2772 S32: -0.0914 S33: -0.1131 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 15 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.7331 0.9031 7.8870 REMARK 3 T TENSOR REMARK 3 T11: 0.2303 T22: 0.2179 REMARK 3 T33: 0.2038 T12: 0.0137 REMARK 3 T13: 0.0020 T23: 0.0392 REMARK 3 L TENSOR REMARK 3 L11: 1.6470 L22: 3.0413 REMARK 3 L33: 6.6298 L12: 1.0668 REMARK 3 L13: 1.1913 L23: 4.4205 REMARK 3 S TENSOR REMARK 3 S11: -0.1461 S12: 0.1255 S13: -0.0280 REMARK 3 S21: -0.3100 S22: 0.3881 S23: -0.1814 REMARK 3 S31: -0.3930 S32: 0.1980 S33: -0.2062 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 33 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.6633 10.0338 16.0972 REMARK 3 T TENSOR REMARK 3 T11: 0.3430 T22: 0.3318 REMARK 3 T33: 0.2266 T12: 0.0352 REMARK 3 T13: -0.0317 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 9.1092 L22: 7.7155 REMARK 3 L33: 6.2482 L12: 3.3262 REMARK 3 L13: -6.0478 L23: 0.0958 REMARK 3 S TENSOR REMARK 3 S11: 0.3029 S12: -0.8512 S13: 0.0979 REMARK 3 S21: 0.4738 S22: -0.0776 S23: -0.0462 REMARK 3 S31: -0.2759 S32: 0.6356 S33: -0.0793 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 40 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.5498 2.4665 17.6165 REMARK 3 T TENSOR REMARK 3 T11: 0.2535 T22: 0.2404 REMARK 3 T33: 0.2372 T12: -0.0002 REMARK 3 T13: -0.0354 T23: -0.0269 REMARK 3 L TENSOR REMARK 3 L11: 8.4678 L22: 3.5465 REMARK 3 L33: 2.6285 L12: 2.4480 REMARK 3 L13: -2.6422 L23: 0.5275 REMARK 3 S TENSOR REMARK 3 S11: 0.0297 S12: -0.3952 S13: -0.0602 REMARK 3 S21: 0.0098 S22: 0.1886 S23: -0.2566 REMARK 3 S31: -0.3553 S32: 0.2958 S33: -0.1429 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.7187 -8.2437 11.0378 REMARK 3 T TENSOR REMARK 3 T11: 0.2451 T22: 0.3821 REMARK 3 T33: 0.4022 T12: 0.0548 REMARK 3 T13: 0.0361 T23: 0.0370 REMARK 3 L TENSOR REMARK 3 L11: 3.5058 L22: 6.1904 REMARK 3 L33: 4.5669 L12: -0.9555 REMARK 3 L13: -1.5093 L23: -0.7504 REMARK 3 S TENSOR REMARK 3 S11: 0.0471 S12: -0.1393 S13: -0.2287 REMARK 3 S21: -0.4733 S22: -0.2824 S23: -0.9159 REMARK 3 S31: 0.0232 S32: 1.0158 S33: 0.0444 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 75 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0982 -17.6040 17.6617 REMARK 3 T TENSOR REMARK 3 T11: 0.3058 T22: 0.2229 REMARK 3 T33: 0.3553 T12: 0.0739 REMARK 3 T13: 0.0290 T23: 0.0219 REMARK 3 L TENSOR REMARK 3 L11: 3.2450 L22: 3.2048 REMARK 3 L33: 1.9580 L12: 3.1267 REMARK 3 L13: 1.1195 L23: 0.5099 REMARK 3 S TENSOR REMARK 3 S11: 0.2615 S12: -0.1724 S13: -0.6461 REMARK 3 S21: 0.3411 S22: -0.1798 S23: -0.2928 REMARK 3 S31: 0.2704 S32: 0.2699 S33: -0.0429 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 90 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.7555 -4.0162 16.5192 REMARK 3 T TENSOR REMARK 3 T11: 0.2096 T22: 0.1581 REMARK 3 T33: 0.1797 T12: 0.0089 REMARK 3 T13: -0.0137 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 6.8020 L22: 2.9863 REMARK 3 L33: 1.8492 L12: -3.2117 REMARK 3 L13: 0.0382 L23: -0.3687 REMARK 3 S TENSOR REMARK 3 S11: -0.1609 S12: -0.2399 S13: -0.0377 REMARK 3 S21: 0.1659 S22: 0.1247 S23: -0.0723 REMARK 3 S31: 0.0376 S32: -0.0087 S33: 0.0764 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.7032 11.8992 6.1007 REMARK 3 T TENSOR REMARK 3 T11: 0.4970 T22: 0.3069 REMARK 3 T33: 0.3614 T12: 0.0264 REMARK 3 T13: 0.0228 T23: 0.0430 REMARK 3 L TENSOR REMARK 3 L11: 5.1025 L22: 0.0765 REMARK 3 L33: 3.8229 L12: -0.4127 REMARK 3 L13: 1.8135 L23: 0.0676 REMARK 3 S TENSOR REMARK 3 S11: -0.2799 S12: 0.0402 S13: 0.6574 REMARK 3 S21: -0.1832 S22: 0.2615 S23: 0.0250 REMARK 3 S31: -0.9757 S32: 0.2988 S33: 0.1747 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 126 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9672 13.7325 18.6230 REMARK 3 T TENSOR REMARK 3 T11: 0.3286 T22: 0.2669 REMARK 3 T33: 0.4603 T12: -0.0418 REMARK 3 T13: -0.0300 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 3.4281 L22: 8.4860 REMARK 3 L33: 5.8061 L12: 3.5078 REMARK 3 L13: -0.7148 L23: 4.3188 REMARK 3 S TENSOR REMARK 3 S11: -0.0467 S12: -0.6608 S13: -0.1840 REMARK 3 S21: -0.0431 S22: 0.4507 S23: -0.6481 REMARK 3 S31: -0.8413 S32: 0.0212 S33: -0.4987 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3725 13.4274 -5.8802 REMARK 3 T TENSOR REMARK 3 T11: 0.3089 T22: 0.2769 REMARK 3 T33: 0.2362 T12: -0.0510 REMARK 3 T13: 0.0582 T23: -0.0328 REMARK 3 L TENSOR REMARK 3 L11: 6.4732 L22: 6.7272 REMARK 3 L33: 2.2379 L12: -1.4760 REMARK 3 L13: 2.1749 L23: 0.9385 REMARK 3 S TENSOR REMARK 3 S11: 0.2037 S12: -0.5418 S13: 0.4014 REMARK 3 S21: 0.7555 S22: 0.0290 S23: 0.3719 REMARK 3 S31: -0.4311 S32: -0.0150 S33: -0.2031 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 15 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2225 3.9948 -5.7075 REMARK 3 T TENSOR REMARK 3 T11: 0.2669 T22: 0.2747 REMARK 3 T33: 0.1688 T12: -0.0737 REMARK 3 T13: 0.0329 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 4.3659 L22: 5.3031 REMARK 3 L33: 3.2871 L12: -0.1918 REMARK 3 L13: -1.1272 L23: -1.0154 REMARK 3 S TENSOR REMARK 3 S11: -0.0518 S12: -0.3714 S13: 0.0510 REMARK 3 S21: 0.4522 S22: 0.2384 S23: -0.0040 REMARK 3 S31: 0.1621 S32: -0.3083 S33: -0.1758 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 28 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6266 -5.4991 -7.0099 REMARK 3 T TENSOR REMARK 3 T11: 0.3675 T22: 0.3163 REMARK 3 T33: 0.3600 T12: -0.0248 REMARK 3 T13: 0.0113 T23: 0.0344 REMARK 3 L TENSOR REMARK 3 L11: 3.0120 L22: 3.0980 REMARK 3 L33: 3.4796 L12: -2.9756 REMARK 3 L13: -0.3574 L23: 1.0182 REMARK 3 S TENSOR REMARK 3 S11: -0.1913 S12: -0.7279 S13: -0.5994 REMARK 3 S21: 0.3080 S22: 0.1921 S23: -0.3202 REMARK 3 S31: 0.4368 S32: -0.0088 S33: -0.0196 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 40 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6855 -0.5003 -9.9137 REMARK 3 T TENSOR REMARK 3 T11: 0.2501 T22: 0.2575 REMARK 3 T33: 0.2838 T12: 0.0178 REMARK 3 T13: 0.0148 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 2.5904 L22: 3.5091 REMARK 3 L33: 5.9542 L12: -2.0194 REMARK 3 L13: 3.4872 L23: -1.4743 REMARK 3 S TENSOR REMARK 3 S11: 0.0278 S12: 0.4818 S13: 0.3623 REMARK 3 S21: 0.0058 S22: -0.0611 S23: -0.4058 REMARK 3 S31: 0.3905 S32: 0.6156 S33: 0.0218 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 58 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5520 10.3209 -0.5705 REMARK 3 T TENSOR REMARK 3 T11: 0.5165 T22: 0.5986 REMARK 3 T33: 0.3853 T12: -0.2551 REMARK 3 T13: -0.1287 T23: 0.0504 REMARK 3 L TENSOR REMARK 3 L11: 1.6568 L22: 3.6826 REMARK 3 L33: 6.0735 L12: 2.0317 REMARK 3 L13: -1.3164 L23: -0.6753 REMARK 3 S TENSOR REMARK 3 S11: 0.6877 S12: -1.0592 S13: -0.0247 REMARK 3 S21: 1.1192 S22: -0.4666 S23: -0.8109 REMARK 3 S31: -0.3675 S32: 1.2007 S33: -0.3281 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 75 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5454 19.6973 -11.5665 REMARK 3 T TENSOR REMARK 3 T11: 0.2828 T22: 0.2192 REMARK 3 T33: 0.3532 T12: -0.0635 REMARK 3 T13: 0.0188 T23: 0.0338 REMARK 3 L TENSOR REMARK 3 L11: 8.2581 L22: 3.1820 REMARK 3 L33: 3.3076 L12: -0.4049 REMARK 3 L13: 0.9270 L23: -0.3145 REMARK 3 S TENSOR REMARK 3 S11: 0.0261 S12: -0.1008 S13: 0.1903 REMARK 3 S21: 0.1890 S22: -0.2837 S23: -0.6436 REMARK 3 S31: -0.2475 S32: 0.1475 S33: 0.2713 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 90 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5285 9.6520 -11.3371 REMARK 3 T TENSOR REMARK 3 T11: 0.2417 T22: 0.2411 REMARK 3 T33: 0.2537 T12: -0.0385 REMARK 3 T13: -0.0057 T23: 0.0420 REMARK 3 L TENSOR REMARK 3 L11: 7.6123 L22: 3.6027 REMARK 3 L33: 3.2081 L12: 3.0010 REMARK 3 L13: 1.8687 L23: 0.8371 REMARK 3 S TENSOR REMARK 3 S11: -0.0344 S12: -0.0376 S13: -0.0445 REMARK 3 S21: 0.2086 S22: -0.0906 S23: -0.3157 REMARK 3 S31: -0.2627 S32: 0.3535 S33: 0.1111 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 109 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1530 -0.6228 -12.9751 REMARK 3 T TENSOR REMARK 3 T11: 0.2956 T22: 0.3069 REMARK 3 T33: 0.2382 T12: -0.0784 REMARK 3 T13: 0.0265 T23: -0.0617 REMARK 3 L TENSOR REMARK 3 L11: 8.5513 L22: 3.4666 REMARK 3 L33: 6.7872 L12: 5.1050 REMARK 3 L13: -2.5838 L23: -3.1401 REMARK 3 S TENSOR REMARK 3 S11: -0.2960 S12: 0.1524 S13: -0.2804 REMARK 3 S21: 0.1957 S22: 0.3290 S23: 0.1935 REMARK 3 S31: 0.7277 S32: -1.0614 S33: 0.0024 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 118 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5526 -7.9603 -2.6519 REMARK 3 T TENSOR REMARK 3 T11: 0.4010 T22: 0.3361 REMARK 3 T33: 0.3309 T12: -0.0475 REMARK 3 T13: 0.0615 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 4.2695 L22: 6.2883 REMARK 3 L33: 3.6195 L12: -5.1717 REMARK 3 L13: 0.1763 L23: -0.0376 REMARK 3 S TENSOR REMARK 3 S11: -0.5958 S12: -0.3636 S13: -0.4995 REMARK 3 S21: 0.6992 S22: 0.6938 S23: 0.3555 REMARK 3 S31: 0.5025 S32: -0.2098 S33: 0.0210 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 126 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.0766 -11.7214 -9.3257 REMARK 3 T TENSOR REMARK 3 T11: 0.4954 T22: 0.3762 REMARK 3 T33: 0.5485 T12: -0.0008 REMARK 3 T13: 0.1242 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 2.7328 L22: 9.4082 REMARK 3 L33: 2.1118 L12: -4.2911 REMARK 3 L13: 1.0152 L23: 0.5571 REMARK 3 S TENSOR REMARK 3 S11: -0.2793 S12: 0.7270 S13: 0.7754 REMARK 3 S21: -0.1582 S22: 0.5027 S23: -0.4719 REMARK 3 S31: 0.8068 S32: 0.0902 S33: -0.2787 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.425 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.25700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3IQ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG4000, 0.1M TRIS HCL, 0.1M REMARK 280 LITHIUM SULFATE, PH 9.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 35.81600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 32 CB CG CD1 CD2 REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 127 CE NZ REMARK 470 LYS B 36 CD CE NZ REMARK 470 LYS B 57 CD CE NZ REMARK 470 LYS B 69 CG CD CE NZ REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 LYS B 122 CD CE NZ REMARK 470 LYS B 129 CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 94 CD REMARK 480 GLU B 94 CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 53 C LYS A 57 N -0.279 REMARK 500 LYS A 127 N LYS A 127 CA -0.261 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 53 CA - C - N ANGL. DEV. = 16.0 DEGREES REMARK 500 LYS A 53 O - C - N ANGL. DEV. = -16.0 DEGREES 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 ALA A 24 76.71 -162.93 REMARK 500 ALA B 24 83.42 -159.17 REMARK 500 LEU B 32 95.15 49.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 419 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH B 389 DISTANCE = 6.36 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GKP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BCT B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH B 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IQ3 RELATED DB: PDB REMARK 900 SAME TOXIN, CRYSTALLIZED WITH PEG4000 DBREF 6DIK A 1 133 UNP Q90249 PA2B1_BOTJR 17 137 DBREF 6DIK B 1 133 UNP Q90249 PA2B1_BOTJR 17 137 SEQADV 6DIK ASN A 67 UNP Q90249 ASP 74 CONFLICT SEQADV 6DIK ASN B 67 UNP Q90249 ASP 74 CONFLICT SEQRES 1 A 121 SER LEU PHE GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 A 121 GLY LYS ASN PRO ALA LYS SER TYR GLY ALA TYR GLY CYS SEQRES 3 A 121 ASN CYS GLY VAL LEU GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 A 121 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 A 121 LYS LEU THR GLY CYS ASN PRO LYS LYS ASP ARG TYR SER SEQRES 6 A 121 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 A 121 ASN PRO CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 A 121 VAL ALA ILE CYS LEU ARG GLU ASN LEU GLY THR TYR ASN SEQRES 9 A 121 LYS LYS TYR ARG TYR HIS LEU LYS PRO PHE CYS LYS LYS SEQRES 10 A 121 ALA ASP PRO CYS SEQRES 1 B 121 SER LEU PHE GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 B 121 GLY LYS ASN PRO ALA LYS SER TYR GLY ALA TYR GLY CYS SEQRES 3 B 121 ASN CYS GLY VAL LEU GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 B 121 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 B 121 LYS LEU THR GLY CYS ASN PRO LYS LYS ASP ARG TYR SER SEQRES 6 B 121 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 B 121 ASN PRO CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 B 121 VAL ALA ILE CYS LEU ARG GLU ASN LEU GLY THR TYR ASN SEQRES 9 B 121 LYS LYS TYR ARG TYR HIS LEU LYS PRO PHE CYS LYS LYS SEQRES 10 B 121 ALA ASP PRO CYS HET GKP A 201 34 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HET SO4 B 201 5 HET SO4 B 202 5 HET BCT B 203 4 HET EOH B 204 3 HETNAM GKP (2R,3R)-2,3-BIS{[(2E)-3-(3,4-DIHYDROXYPHENYL)PROP-2- HETNAM 2 GKP ENOYL]OXY}BUTANEDIOIC ACID HETNAM SO4 SULFATE ION HETNAM BCT BICARBONATE ION HETNAM EOH ETHANOL FORMUL 3 GKP C22 H18 O12 FORMUL 4 SO4 5(O4 S 2-) FORMUL 9 BCT C H O3 1- FORMUL 10 EOH C2 H6 O FORMUL 11 HOH *208(H2 O) HELIX 1 AA1 SER A 1 GLY A 15 1 14 HELIX 2 AA2 ASN A 17 GLY A 23 1 7 HELIX 3 AA3 ASP A 39 LYS A 57 1 16 HELIX 4 AA4 ASN A 88 ASN A 109 1 21 HELIX 5 AA5 LEU A 110 TYR A 113 5 4 HELIX 6 AA6 ASN A 114 ARG A 118 5 5 HELIX 7 AA7 LEU A 121 CYS A 126 5 5 HELIX 8 AA8 LEU B 2 GLY B 15 1 13 HELIX 9 AA9 ASN B 17 GLY B 23 1 7 HELIX 10 AB1 ASP B 39 LYS B 57 1 16 HELIX 11 AB2 ASN B 88 ASN B 109 1 21 HELIX 12 AB3 LEU B 110 TYR B 113 5 4 HELIX 13 AB4 ASN B 114 ARG B 118 5 5 HELIX 14 AB5 LEU B 121 CYS B 126 5 5 SHEET 1 AA1 2 TYR A 75 LYS A 78 0 SHEET 2 AA1 2 THR A 81 CYS A 84 -1 O VAL A 83 N SER A 76 SHEET 1 AA2 2 ALA B 24 TYR B 25 0 SHEET 2 AA2 2 CYS B 29 GLY B 30 -1 O CYS B 29 N TYR B 25 SHEET 1 AA3 2 TYR B 75 LYS B 78 0 SHEET 2 AA3 2 THR B 81 CYS B 84 -1 O VAL B 83 N SER B 76 SSBOND 1 CYS A 27 CYS A 126 1555 1555 2.04 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.04 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.04 SSBOND 4 CYS A 50 CYS A 133 1555 1555 2.04 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.04 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.03 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.03 SSBOND 8 CYS B 27 CYS B 126 1555 1555 2.03 SSBOND 9 CYS B 29 CYS B 45 1555 1555 2.05 SSBOND 10 CYS B 44 CYS B 105 1555 1555 2.04 SSBOND 11 CYS B 50 CYS B 133 1555 1555 2.04 SSBOND 12 CYS B 51 CYS B 98 1555 1555 2.04 SSBOND 13 CYS B 61 CYS B 91 1555 1555 2.04 SSBOND 14 CYS B 84 CYS B 96 1555 1555 2.03 SITE 1 AC1 11 LEU A 2 PHE A 3 GLY A 6 LYS A 7 SITE 2 AC1 11 PRO A 18 HOH A 302 HOH A 305 HOH A 306 SITE 3 AC1 11 HOH A 322 HOH A 325 PRO B 123 SITE 1 AC2 4 LYS A 20 LYS A 115 ARG A 118 SO4 A 203 SITE 1 AC3 7 LYS A 16 ASN A 17 LYS A 20 SO4 A 202 SITE 2 AC3 7 HOH A 301 HOH A 315 HOH A 359 SITE 1 AC4 3 ARG A 34 LYS A 53 HOH A 341 SITE 1 AC5 3 GLY B 33 ARG B 34 LYS B 53 SITE 1 AC6 3 THR B 59 LYS B 115 ARG B 118 SITE 1 AC7 1 ARG B 107 SITE 1 AC8 1 PRO B 18 CRYST1 39.558 71.632 44.791 90.00 109.02 90.00 P 1 21 1 4 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 0.025279 0.000000 0.008714 0.00000 SCALE2 0.000000 0.013960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023615 0.00000