HEADER OXIDOREDUCTASE 30-JAN-22 7QYZ TITLE CRYSTAL STRUCTURE OF A DYP-TYPE PEROXIDASE 6E10 VARIANT FROM TITLE 2 PSEUDOMONAS PUTIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DYP-TYPE PEROXIDASE FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 STRAIN: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440; SOURCE 5 GENE: PP_3248; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DYP, HEME, PSEUDOMONAS PUTIDA, DIRECTED EVOLUTION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.T.BORGES,D.SILVA,L.O.MARTINS,C.FRAZAO REVDAT 3 01-MAY-24 7QYZ 1 REMARK REVDAT 2 24-AUG-22 7QYZ 1 JRNL REVDAT 1 03-AUG-22 7QYZ 0 JRNL AUTH P.T.BORGES,D.SILVA,T.F.D.SILVA,V.BRISSOS,M.CANELLAS, JRNL AUTH 2 M.F.LUCAS,L.MASGRAU,E.P.MELO,M.MACHUQUEIRO,C.FRAZAO, JRNL AUTH 3 L.O.MARTINS JRNL TITL UNVEILING MOLECULAR DETAILS BEHIND IMPROVED ACTIVITY AT JRNL TITL 2 NEUTRAL TO ALKALINE PH OF AN ENGINEERED DYP-TYPE PEROXIDASE. JRNL REF COMPUT STRUCT BIOTECHNOL J V. 20 3899 2022 JRNL REFN ESSN 2001-0370 JRNL PMID 35950185 JRNL DOI 10.1016/J.CSBJ.2022.07.032 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : LS_WUNIT_K1 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 14985 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 100.00 REMARK 3 FREE R VALUE TEST SET COUNT : 14985 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 48.6220 - 7.6095 0.97 574 574 0.1595 0.1595 REMARK 3 2 7.6095 - 6.0436 0.99 546 546 0.1963 0.1963 REMARK 3 3 6.0436 - 5.2807 0.99 539 539 0.2225 0.2225 REMARK 3 4 5.2807 - 4.7983 0.97 535 535 0.1847 0.1847 REMARK 3 5 4.7983 - 4.4546 0.99 542 542 0.1644 0.1644 REMARK 3 6 4.4546 - 4.1922 1.00 515 515 0.1787 0.1787 REMARK 3 7 4.1922 - 3.9823 1.00 549 549 0.1870 0.1870 REMARK 3 8 3.9823 - 3.8090 0.75 405 405 0.2127 0.2127 REMARK 3 9 3.8090 - 3.6624 0.99 374 374 0.2055 0.2055 REMARK 3 10 3.6624 - 3.5361 0.98 508 508 0.2296 0.2296 REMARK 3 11 3.5361 - 3.4256 0.62 324 324 0.2344 0.2344 REMARK 3 12 3.4256 - 3.3277 1.00 538 538 0.2471 0.2471 REMARK 3 13 3.3277 - 3.2401 1.00 534 534 0.2573 0.2573 REMARK 3 14 3.2401 - 3.1610 1.00 530 530 0.2815 0.2815 REMARK 3 15 3.1610 - 3.0892 1.00 530 530 0.3019 0.3019 REMARK 3 16 3.0892 - 3.0235 1.00 522 522 0.3034 0.3034 REMARK 3 17 3.0235 - 2.9630 1.00 521 521 0.3101 0.3101 REMARK 3 18 2.9630 - 2.9071 1.00 539 539 0.2977 0.2977 REMARK 3 19 2.9071 - 2.8552 1.00 517 517 0.2944 0.2944 REMARK 3 20 2.8552 - 2.8068 1.00 532 532 0.3103 0.3103 REMARK 3 21 2.8068 - 2.7615 1.00 549 549 0.3080 0.3080 REMARK 3 22 2.7615 - 2.7190 0.99 499 499 0.3365 0.3365 REMARK 3 23 2.7190 - 2.6790 0.96 228 228 0.3450 0.3450 REMARK 3 24 2.6790 - 2.6413 0.97 385 385 0.4203 0.4203 REMARK 3 25 2.6413 - 2.6056 1.00 510 510 0.3523 0.3523 REMARK 3 26 2.6056 - 2.5718 1.00 540 540 0.3543 0.3543 REMARK 3 27 2.5718 - 2.5396 1.00 510 510 0.3705 0.3705 REMARK 3 28 2.5396 - 2.5090 1.00 527 527 0.3627 0.3627 REMARK 3 29 2.5090 - 2.4799 1.00 517 517 0.3721 0.3721 REMARK 3 30 2.4799 - 2.4520 1.00 546 546 0.3810 0.3810 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.79 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 17 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 4:13) REMARK 3 ORIGIN FOR THE GROUP (A): 37.6020 26.9684 -5.1310 REMARK 3 T TENSOR REMARK 3 T11: 1.0170 T22: 0.4191 REMARK 3 T33: 0.7392 T12: -0.2809 REMARK 3 T13: 0.4084 T23: 0.1104 REMARK 3 L TENSOR REMARK 3 L11: 0.1539 L22: 0.0872 REMARK 3 L33: 0.1825 L12: -0.1208 REMARK 3 L13: -0.1008 L23: 0.1324 REMARK 3 S TENSOR REMARK 3 S11: -0.5729 S12: 0.2274 S13: -0.4410 REMARK 3 S21: -0.1254 S22: 0.3107 S23: 0.0881 REMARK 3 S31: 0.1798 S32: 0.3858 S33: 0.0339 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 14:34) REMARK 3 ORIGIN FOR THE GROUP (A): 40.2693 45.1835 -15.3521 REMARK 3 T TENSOR REMARK 3 T11: 0.7855 T22: 0.6521 REMARK 3 T33: 0.3582 T12: -0.3572 REMARK 3 T13: 0.0434 T23: 0.0782 REMARK 3 L TENSOR REMARK 3 L11: 0.4737 L22: 0.3814 REMARK 3 L33: 0.3920 L12: -0.3988 REMARK 3 L13: -0.2928 L23: 0.0619 REMARK 3 S TENSOR REMARK 3 S11: -0.6133 S12: 0.0555 S13: -0.1015 REMARK 3 S21: -0.5514 S22: 0.7527 S23: -0.2605 REMARK 3 S31: -0.0052 S32: 0.3508 S33: 0.1051 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 35:56) REMARK 3 ORIGIN FOR THE GROUP (A): 36.0283 38.4530 -15.3137 REMARK 3 T TENSOR REMARK 3 T11: 0.9156 T22: 0.6544 REMARK 3 T33: 0.7121 T12: -0.3135 REMARK 3 T13: 0.0047 T23: 0.1021 REMARK 3 L TENSOR REMARK 3 L11: 0.1157 L22: 0.0584 REMARK 3 L33: 0.0088 L12: 0.1261 REMARK 3 L13: 0.0339 L23: 0.0284 REMARK 3 S TENSOR REMARK 3 S11: -0.4518 S12: 0.1521 S13: -0.3854 REMARK 3 S21: -0.6938 S22: 0.5357 S23: 0.3250 REMARK 3 S31: 0.2031 S32: -0.1773 S33: 0.0685 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 57:63) REMARK 3 ORIGIN FOR THE GROUP (A): 22.1593 44.5040 -16.1502 REMARK 3 T TENSOR REMARK 3 T11: 0.9513 T22: 0.7548 REMARK 3 T33: 0.7656 T12: -0.3199 REMARK 3 T13: -0.0872 T23: 0.2613 REMARK 3 L TENSOR REMARK 3 L11: 0.0147 L22: -0.0002 REMARK 3 L33: 0.0097 L12: 0.0082 REMARK 3 L13: -0.0179 L23: -0.0134 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: 0.0989 S13: -0.1302 REMARK 3 S21: 0.1313 S22: -0.0337 S23: 0.1248 REMARK 3 S31: 0.0485 S32: -0.6113 S33: -0.0065 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 64:89) REMARK 3 ORIGIN FOR THE GROUP (A): 32.8131 46.1859 -1.7730 REMARK 3 T TENSOR REMARK 3 T11: 0.6521 T22: 0.5538 REMARK 3 T33: 0.6390 T12: -0.0947 REMARK 3 T13: 0.0599 T23: 0.2305 REMARK 3 L TENSOR REMARK 3 L11: 0.2366 L22: 0.5384 REMARK 3 L33: 0.5222 L12: 0.0219 REMARK 3 L13: 0.1348 L23: 0.1384 REMARK 3 S TENSOR REMARK 3 S11: -0.4377 S12: -0.0245 S13: -0.2041 REMARK 3 S21: 0.0607 S22: 0.5879 S23: 0.4595 REMARK 3 S31: 0.0001 S32: 0.0432 S33: 0.2506 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 90:103) REMARK 3 ORIGIN FOR THE GROUP (A): 51.5529 37.7028 -10.9745 REMARK 3 T TENSOR REMARK 3 T11: 0.7547 T22: 0.7157 REMARK 3 T33: 0.4605 T12: -0.2649 REMARK 3 T13: 0.2315 T23: -0.1157 REMARK 3 L TENSOR REMARK 3 L11: 0.1293 L22: -0.0174 REMARK 3 L33: -0.0017 L12: -0.0862 REMARK 3 L13: -0.0595 L23: -0.0341 REMARK 3 S TENSOR REMARK 3 S11: -0.3102 S12: 0.0432 S13: 0.0710 REMARK 3 S21: -0.6316 S22: 0.5059 S23: -0.1050 REMARK 3 S31: 0.1699 S32: 0.3793 S33: 0.0001 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 104:123) REMARK 3 ORIGIN FOR THE GROUP (A): 45.7924 42.2604 -6.8726 REMARK 3 T TENSOR REMARK 3 T11: 0.7789 T22: 0.6062 REMARK 3 T33: 0.5427 T12: -0.1950 REMARK 3 T13: 0.0964 T23: 0.1157 REMARK 3 L TENSOR REMARK 3 L11: 0.1663 L22: 0.0797 REMARK 3 L33: 0.0775 L12: -0.0155 REMARK 3 L13: -0.1920 L23: 0.0312 REMARK 3 S TENSOR REMARK 3 S11: -0.5904 S12: 0.1784 S13: -0.2341 REMARK 3 S21: -0.1436 S22: 0.0534 S23: -0.0977 REMARK 3 S31: -0.0872 S32: 0.5531 S33: -0.0921 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 124:131) REMARK 3 ORIGIN FOR THE GROUP (A): 43.9591 33.3408 13.3049 REMARK 3 T TENSOR REMARK 3 T11: 0.6549 T22: 0.5803 REMARK 3 T33: 0.6480 T12: 0.1848 REMARK 3 T13: 0.2436 T23: 0.2210 REMARK 3 L TENSOR REMARK 3 L11: 0.0035 L22: 0.0251 REMARK 3 L33: 0.0040 L12: -0.0091 REMARK 3 L13: -0.0088 L23: -0.0091 REMARK 3 S TENSOR REMARK 3 S11: -0.3915 S12: -0.4899 S13: -0.0755 REMARK 3 S21: -0.0622 S22: 0.1017 S23: 0.2676 REMARK 3 S31: 0.1228 S32: 0.2414 S33: 0.0001 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 132:142) REMARK 3 ORIGIN FOR THE GROUP (A): 31.6503 24.8533 5.9647 REMARK 3 T TENSOR REMARK 3 T11: 1.2707 T22: 0.9063 REMARK 3 T33: 1.6895 T12: -0.2523 REMARK 3 T13: 0.2458 T23: 0.2864 REMARK 3 L TENSOR REMARK 3 L11: 0.0271 L22: 0.0145 REMARK 3 L33: 0.0282 L12: -0.0256 REMARK 3 L13: -0.0188 L23: -0.0068 REMARK 3 S TENSOR REMARK 3 S11: -0.1379 S12: 0.0582 S13: -0.1068 REMARK 3 S21: -0.0956 S22: -0.1332 S23: -0.2406 REMARK 3 S31: 0.2329 S32: 0.0982 S33: -0.0001 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 143:151) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5072 28.0256 -6.1570 REMARK 3 T TENSOR REMARK 3 T11: 0.9177 T22: 0.7303 REMARK 3 T33: 1.4552 T12: -0.5974 REMARK 3 T13: 0.1306 T23: 0.5534 REMARK 3 L TENSOR REMARK 3 L11: 0.1492 L22: 0.1938 REMARK 3 L33: 0.1451 L12: 0.0886 REMARK 3 L13: -0.0543 L23: -0.1586 REMARK 3 S TENSOR REMARK 3 S11: -0.0228 S12: 0.1683 S13: 0.0191 REMARK 3 S21: 0.0456 S22: -0.0100 S23: 0.0621 REMARK 3 S31: 0.0926 S32: -0.1637 S33: -0.0556 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 152:185) REMARK 3 ORIGIN FOR THE GROUP (A): 40.2835 39.6973 15.3888 REMARK 3 T TENSOR REMARK 3 T11: 0.6982 T22: 0.7435 REMARK 3 T33: 0.5652 T12: 0.2312 REMARK 3 T13: 0.3098 T23: 0.3142 REMARK 3 L TENSOR REMARK 3 L11: 0.5760 L22: 1.0749 REMARK 3 L33: 1.3879 L12: 0.5471 REMARK 3 L13: 0.4750 L23: 0.3919 REMARK 3 S TENSOR REMARK 3 S11: -0.6759 S12: -0.2257 S13: -0.1715 REMARK 3 S21: 0.1133 S22: 0.3917 S23: 0.3738 REMARK 3 S31: -0.0927 S32: 0.4197 S33: -0.4037 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 186:207) REMARK 3 ORIGIN FOR THE GROUP (A): 28.3591 34.2817 18.7710 REMARK 3 T TENSOR REMARK 3 T11: 0.4507 T22: 0.7700 REMARK 3 T33: 0.7940 T12: 0.1813 REMARK 3 T13: 0.4369 T23: 0.5396 REMARK 3 L TENSOR REMARK 3 L11: 0.5653 L22: 0.3892 REMARK 3 L33: -0.0283 L12: 0.3234 REMARK 3 L13: -0.1160 L23: -0.0918 REMARK 3 S TENSOR REMARK 3 S11: -0.3888 S12: 0.9827 S13: 0.0170 REMARK 3 S21: 0.8371 S22: 0.5633 S23: 0.1706 REMARK 3 S31: -0.0337 S32: -0.7884 S33: -0.0216 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 208:212) REMARK 3 ORIGIN FOR THE GROUP (A): 22.1773 33.0988 6.6465 REMARK 3 T TENSOR REMARK 3 T11: 0.9006 T22: 0.7387 REMARK 3 T33: 1.3465 T12: -0.1509 REMARK 3 T13: 0.5613 T23: 0.6443 REMARK 3 L TENSOR REMARK 3 L11: 0.0017 L22: 0.0552 REMARK 3 L33: 0.0321 L12: -0.0026 REMARK 3 L13: 0.0121 L23: -0.0336 REMARK 3 S TENSOR REMARK 3 S11: 0.0148 S12: -0.0388 S13: -0.0225 REMARK 3 S21: -0.0296 S22: -0.0029 S23: -0.1761 REMARK 3 S31: -0.1404 S32: -0.1589 S33: -0.1008 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 213:233) REMARK 3 ORIGIN FOR THE GROUP (A): 41.1683 39.5674 3.1311 REMARK 3 T TENSOR REMARK 3 T11: 0.6379 T22: 0.5327 REMARK 3 T33: 0.6284 T12: 0.0470 REMARK 3 T13: 0.3036 T23: 0.4117 REMARK 3 L TENSOR REMARK 3 L11: 0.2170 L22: 0.2504 REMARK 3 L33: 0.0292 L12: -0.0919 REMARK 3 L13: -0.1106 L23: -0.0961 REMARK 3 S TENSOR REMARK 3 S11: -0.4887 S12: -0.8885 S13: -0.2446 REMARK 3 S21: 0.1444 S22: 0.3660 S23: -0.0394 REMARK 3 S31: 0.0343 S32: 0.0002 S33: 0.0575 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 234:245) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0264 40.6485 4.7832 REMARK 3 T TENSOR REMARK 3 T11: 0.5365 T22: 0.7428 REMARK 3 T33: 0.9737 T12: 0.0306 REMARK 3 T13: 0.2761 T23: 0.4755 REMARK 3 L TENSOR REMARK 3 L11: 0.3373 L22: 0.1687 REMARK 3 L33: 0.8062 L12: -0.1307 REMARK 3 L13: 0.4572 L23: 0.0012 REMARK 3 S TENSOR REMARK 3 S11: -1.0161 S12: -0.1300 S13: 0.0346 REMARK 3 S21: 0.2458 S22: -0.3682 S23: 0.5678 REMARK 3 S31: 0.3290 S32: -0.2900 S33: -0.2525 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: (CHAIN A AND RESID 246:263) REMARK 3 ORIGIN FOR THE GROUP (A): 31.3936 46.5813 15.0229 REMARK 3 T TENSOR REMARK 3 T11: 0.7668 T22: 0.6848 REMARK 3 T33: 0.6847 T12: 0.4497 REMARK 3 T13: 0.3018 T23: 0.5754 REMARK 3 L TENSOR REMARK 3 L11: 0.1816 L22: 1.7842 REMARK 3 L33: 1.8588 L12: -0.0481 REMARK 3 L13: 0.0149 L23: 0.8158 REMARK 3 S TENSOR REMARK 3 S11: -0.2700 S12: -0.5964 S13: 0.1548 REMARK 3 S21: -0.0263 S22: 1.0059 S23: 0.4052 REMARK 3 S31: -0.4932 S32: -0.2286 S33: 1.0156 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: (CHAIN A AND RESID 264:285) REMARK 3 ORIGIN FOR THE GROUP (A): 30.3383 37.4425 -13.5836 REMARK 3 T TENSOR REMARK 3 T11: 0.7239 T22: 0.5223 REMARK 3 T33: 0.6730 T12: -0.4262 REMARK 3 T13: -0.0043 T23: 0.3033 REMARK 3 L TENSOR REMARK 3 L11: 0.4755 L22: 0.6615 REMARK 3 L33: 0.3096 L12: -0.5758 REMARK 3 L13: -0.0118 L23: 0.3559 REMARK 3 S TENSOR REMARK 3 S11: -0.3717 S12: -0.0670 S13: -0.1710 REMARK 3 S21: 0.1302 S22: 0.4903 S23: 0.3676 REMARK 3 S31: 0.5504 S32: -0.4694 S33: 0.1422 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE REFINEMENT CONVERGED TO RWORK REMARK 3 AND R-FREE OF 0.222 AND 0.255, RESPECTIVELY. THE FINAL MODEL WAS REMARK 3 THEN REFINED VERSUS THE FULL DATA SET. REMARK 4 REMARK 4 7QYZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14987 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 48.622 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PPDYP WT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.075 M SODIUM BROMIDE, 0.05 M SODIUM REMARK 280 FLUORIDE, 0.1 M HEPES PH 7.8, 22.5 % V/V PEG SMEAR BROAD AND REMARK 280 0.075 M SODIUM IODIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 108.72100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 108.72100 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 108.72100 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 108.72100 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 PHE A 3 REMARK 465 ARG A 286 REMARK 465 ALA A 287 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 THR A 79 59.62 -107.89 REMARK 500 ALA A 148 -156.88 -91.58 REMARK 500 ASP A 163 77.82 -105.45 REMARK 500 ASP A 185 9.64 -152.79 REMARK 500 ALA A 202 109.70 -58.17 REMARK 500 ALA A 210 -158.69 -111.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 197 NE2 REMARK 620 2 HEM A 301 NA 83.9 REMARK 620 3 HEM A 301 NB 84.3 89.5 REMARK 620 4 HEM A 301 NC 100.0 176.0 89.9 REMARK 620 5 HEM A 301 ND 97.7 89.8 177.9 90.6 REMARK 620 N 1 2 3 4 DBREF 7QYZ A 1 287 UNP Q88HV5 Q88HV5_PSEPK 1 287 SEQADV 7QYZ TYR A 125 UNP Q88HV5 HIS 125 ENGINEERED MUTATION SEQADV 7QYZ VAL A 142 UNP Q88HV5 ALA 142 ENGINEERED MUTATION SEQADV 7QYZ LYS A 188 UNP Q88HV5 GLU 188 ENGINEERED MUTATION SEQRES 1 A 287 MET PRO PHE GLN GLN GLY LEU LEU ALA THR PRO VAL PRO SEQRES 2 A 287 ALA HIS ALA ARG HIS LEU PHE PHE THR LEU GLN SER PRO SEQRES 3 A 287 GLU ALA LEU PRO ALA ALA LEU ASP ALA LEU LEU PRO GLN SEQRES 4 A 287 VAL ASP GLY LYS GLN LEU LEU LEU GLY VAL GLY ALA PRO SEQRES 5 A 287 LEU ALA LYS ALA LEU GLY ARG GLU ILE PRO GLY LEU ARG SEQRES 6 A 287 PRO PHE PRO LEU LEU ASP ALA ALA VAL GLU ASN PRO SER SEQRES 7 A 287 THR GLN HIS ALA LEU TRP LEU TRP LEU ARG GLY ASP GLU SEQRES 8 A 287 ARG GLY ASP LEU LEU LEU ARG THR GLN ALA LEU GLU GLN SEQRES 9 A 287 ALA LEU ALA PRO ALA LEU SER LEU ALA ASP SER VAL ASP SEQRES 10 A 287 GLY PHE LEU HIS ARG GLY GLY TYR ASP LEU THR GLY TYR SEQRES 11 A 287 GLU ASP GLY THR GLU ASN PRO THR ASP GLU GLU VAL VAL SEQRES 12 A 287 GLN ALA ALA ILE ALA ALA ASP GLY SER SER PHE ALA ALA SEQRES 13 A 287 PHE GLN LEU TRP LYS HIS ASP LEU GLN TYR PHE LYS SER SEQRES 14 A 287 LEU PRO GLN ALA ASP GLN ASP ASN ILE ILE GLY ARG ARG SEQRES 15 A 287 LEU SER ASP ASN GLU LYS LEU ASP ASP ALA PRO ALA SER SEQRES 16 A 287 ALA HIS VAL LYS ARG THR ALA GLN GLU SER PHE GLU PRO SEQRES 17 A 287 GLU ALA PHE MET VAL ARG ARG SER VAL SER TRP ALA ASP SEQRES 18 A 287 GLN ARG GLY ALA GLY LEU ALA PHE VAL ALA LEU GLY LYS SEQRES 19 A 287 SER PHE GLU ALA PHE GLU VAL GLN LEU ARG ARG MET SER SEQRES 20 A 287 GLY LEU GLU ASP GLY ILE ILE ASP GLY LEU TYR ARG PHE SEQRES 21 A 287 SER ARG PRO LEU THR GLY GLY TYR TYR TRP CYS PRO PRO SEQRES 22 A 287 MET SER GLU THR GLY VAL ASP LEU SER PRO LEU LEU ARG SEQRES 23 A 287 ALA HET HEM A 301 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *(H2 O) HELIX 1 AA1 SER A 25 GLU A 27 5 3 HELIX 2 AA2 ALA A 28 LEU A 37 1 10 HELIX 3 AA3 PRO A 38 VAL A 40 5 3 HELIX 4 AA4 ALA A 51 LEU A 57 1 7 HELIX 5 AA5 GLU A 91 ALA A 107 1 17 HELIX 6 AA6 HIS A 121 GLY A 124 5 4 HELIX 7 AA7 GLU A 141 ILE A 147 1 7 HELIX 8 AA8 ASP A 163 LYS A 168 1 6 HELIX 9 AA9 PRO A 171 GLY A 180 1 10 HELIX 10 AB1 ALA A 196 THR A 201 1 6 HELIX 11 AB2 PHE A 236 SER A 247 1 12 HELIX 12 AB3 ASP A 255 ARG A 259 5 5 HELIX 13 AB4 LEU A 281 LEU A 285 5 5 SHEET 1 AA1 4 VAL A 213 ARG A 214 0 SHEET 2 AA1 4 GLY A 224 LEU A 232 -1 O LEU A 232 N VAL A 213 SHEET 3 AA1 4 SER A 153 HIS A 162 -1 N HIS A 162 O ALA A 225 SHEET 4 AA1 4 SER A 261 PRO A 263 -1 O ARG A 262 N LYS A 161 SHEET 1 AA210 VAL A 213 ARG A 214 0 SHEET 2 AA210 GLY A 224 LEU A 232 -1 O LEU A 232 N VAL A 213 SHEET 3 AA210 VAL A 217 ASP A 221 -1 N VAL A 217 O ALA A 228 SHEET 4 AA210 LEU A 110 PHE A 119 -1 N PHE A 119 O SER A 218 SHEET 5 AA210 HIS A 15 LEU A 23 -1 N PHE A 20 O ALA A 113 SHEET 6 AA210 LEU A 83 GLY A 89 -1 O LEU A 87 N ARG A 17 SHEET 7 AA210 LEU A 45 GLY A 50 -1 N LEU A 46 O TRP A 86 SHEET 8 AA210 GLY A 267 CYS A 271 -1 O TRP A 270 N VAL A 49 SHEET 9 AA210 SER A 153 HIS A 162 -1 N SER A 153 O CYS A 271 SHEET 10 AA210 SER A 261 PRO A 263 -1 O ARG A 262 N LYS A 161 LINK NE2 HIS A 197 FE HEM A 301 1555 1555 2.10 CISPEP 1 THR A 10 PRO A 11 0 0.79 CISPEP 2 ALA A 107 PRO A 108 0 1.33 CRYST1 108.721 108.721 108.721 90.00 90.00 90.00 P 2 3 12 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 0.009198 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009198 0.00000