HEADER OXIDOREDUCTASE 27-DEC-19 6VDY TITLE CRYSTAL STRUCTURE OF DEHALOPEROXIDASE B WILD TYPE IN COMPLEX WITH TITLE 2 SUBSTRATE TRICHLOROPHENOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEHALOPEROXIDASE B; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AMPHITRITE ORNATA; SOURCE 3 ORGANISM_TAXID: 129555; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: GOLD(DE3)PLYSS KEYWDS HEME PEROXIDASE, PEROXYGENASE, HEME COFACTOR, OXYGEN BINDING, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.A.GHILADI,V.S.DE SERRANO,A.MCGUIRE,T.MALEWSCHIK REVDAT 2 11-OCT-23 6VDY 1 REMARK REVDAT 1 30-DEC-20 6VDY 0 JRNL AUTH A.H.MCGUIRE,A.R.PETIT,J.KANG,T.MALEWSCHIK,V.DE SERRANO, JRNL AUTH 2 L.M.CAREY,R.A.GHILADI JRNL TITL NONNATIVE HEME INCORPORATION INTO MULTIFUNCTIONAL GLOBIN JRNL TITL 2 INCREASES PEROXYGENASE ACTIVITY AN ORDER AND MAGNITUDE JRNL TITL 3 COMPARED TO NATIVE ENZYME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3714 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 30258 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1453 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 37.2600 - 3.6600 0.96 2964 168 0.1722 0.1962 REMARK 3 2 3.6600 - 2.9100 0.98 2898 144 0.1737 0.2092 REMARK 3 3 2.9100 - 2.5400 0.99 2920 125 0.1803 0.2020 REMARK 3 4 2.5400 - 2.3100 0.99 2852 164 0.1699 0.2059 REMARK 3 5 2.3100 - 2.1400 0.99 2864 142 0.1758 0.2203 REMARK 3 6 2.1400 - 2.0200 0.99 2876 141 0.1826 0.2431 REMARK 3 7 2.0200 - 1.9200 0.99 2843 150 0.1918 0.2390 REMARK 3 8 1.9200 - 1.8300 1.00 2867 145 0.2033 0.2662 REMARK 3 9 1.8300 - 1.7600 1.00 2894 131 0.2054 0.2768 REMARK 3 10 1.7600 - 1.7000 0.99 2827 143 0.2158 0.2654 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) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.509 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.06 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 : 0.016 2650 REMARK 3 ANGLE : 1.444 3659 REMARK 3 CHIRALITY : 0.078 366 REMARK 3 PLANARITY : 0.008 489 REMARK 3 DIHEDRAL : 21.871 395 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 20 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:26) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1880 -2.0751 -23.7954 REMARK 3 T TENSOR REMARK 3 T11: 0.1383 T22: 0.1552 REMARK 3 T33: 0.1560 T12: -0.0136 REMARK 3 T13: -0.0008 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 3.7703 L22: 2.4169 REMARK 3 L33: 3.8796 L12: -1.8275 REMARK 3 L13: 1.1531 L23: -1.2463 REMARK 3 S TENSOR REMARK 3 S11: -0.0987 S12: -0.2437 S13: -0.2821 REMARK 3 S21: 0.0772 S22: 0.1161 S23: 0.2129 REMARK 3 S31: 0.0104 S32: -0.2990 S33: -0.0069 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 27:33) REMARK 3 ORIGIN FOR THE GROUP (A): 16.7604 -3.9899 -15.1311 REMARK 3 T TENSOR REMARK 3 T11: 0.1516 T22: 0.3434 REMARK 3 T33: 0.2632 T12: 0.0091 REMARK 3 T13: 0.0048 T23: 0.0690 REMARK 3 L TENSOR REMARK 3 L11: 8.3009 L22: 9.1164 REMARK 3 L33: 8.9625 L12: -1.1645 REMARK 3 L13: 4.1042 L23: 3.7378 REMARK 3 S TENSOR REMARK 3 S11: -0.4322 S12: -0.4700 S13: 0.6172 REMARK 3 S21: 0.4983 S22: 0.1563 S23: -0.1957 REMARK 3 S31: -0.1728 S32: 0.6936 S33: 0.2793 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 34:37) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4915 -1.1440 -7.5543 REMARK 3 T TENSOR REMARK 3 T11: 0.5364 T22: 0.6212 REMARK 3 T33: 0.6714 T12: -0.1707 REMARK 3 T13: 0.0599 T23: -0.1380 REMARK 3 L TENSOR REMARK 3 L11: 3.6346 L22: 8.9904 REMARK 3 L33: 3.9602 L12: 4.8096 REMARK 3 L13: 3.1082 L23: 2.3857 REMARK 3 S TENSOR REMARK 3 S11: 0.0691 S12: -0.0208 S13: 0.5624 REMARK 3 S21: 0.4967 S22: -0.1795 S23: -0.1648 REMARK 3 S31: -0.6120 S32: 0.6048 S33: 0.0601 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 38:60) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4563 -5.3987 -10.7301 REMARK 3 T TENSOR REMARK 3 T11: 0.3220 T22: 0.2680 REMARK 3 T33: 0.2420 T12: 0.0601 REMARK 3 T13: 0.1030 T23: 0.0437 REMARK 3 L TENSOR REMARK 3 L11: 2.3472 L22: 8.5996 REMARK 3 L33: 1.8285 L12: -2.7265 REMARK 3 L13: 0.1477 L23: -1.1025 REMARK 3 S TENSOR REMARK 3 S11: -0.5372 S12: -0.5572 S13: -0.3649 REMARK 3 S21: 0.9956 S22: 0.3865 S23: 0.5439 REMARK 3 S31: 0.1591 S32: -0.0192 S33: 0.1395 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 61:83) REMARK 3 ORIGIN FOR THE GROUP (A): 1.6736 12.4721 -25.6485 REMARK 3 T TENSOR REMARK 3 T11: 0.3649 T22: 0.2254 REMARK 3 T33: 0.2099 T12: -0.0592 REMARK 3 T13: -0.0205 T23: -0.0424 REMARK 3 L TENSOR REMARK 3 L11: 2.3849 L22: 1.0790 REMARK 3 L33: 0.7477 L12: 0.6010 REMARK 3 L13: -1.2913 L23: -0.1349 REMARK 3 S TENSOR REMARK 3 S11: 0.3474 S12: -0.3331 S13: 0.2922 REMARK 3 S21: 0.4465 S22: -0.2405 S23: 0.1441 REMARK 3 S31: -0.8000 S32: 0.4969 S33: -0.0688 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 84:90) REMARK 3 ORIGIN FOR THE GROUP (A): 8.9791 12.6861 -12.0830 REMARK 3 T TENSOR REMARK 3 T11: 1.2895 T22: 0.9206 REMARK 3 T33: 0.7494 T12: -0.5221 REMARK 3 T13: -0.1754 T23: -0.1134 REMARK 3 L TENSOR REMARK 3 L11: 1.6348 L22: 7.1930 REMARK 3 L33: 9.3306 L12: 1.8024 REMARK 3 L13: -2.4009 L23: -0.6150 REMARK 3 S TENSOR REMARK 3 S11: 0.1455 S12: -0.3551 S13: -0.1433 REMARK 3 S21: 0.9399 S22: -0.2676 S23: 0.0258 REMARK 3 S31: 0.2559 S32: 0.1498 S33: 0.0466 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 91:99) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5661 5.5694 -19.9563 REMARK 3 T TENSOR REMARK 3 T11: 0.5097 T22: 0.3700 REMARK 3 T33: 0.4730 T12: -0.1524 REMARK 3 T13: -0.2005 T23: 0.1247 REMARK 3 L TENSOR REMARK 3 L11: 2.6968 L22: 5.4625 REMARK 3 L33: 8.6699 L12: -2.8383 REMARK 3 L13: -1.7356 L23: 0.0686 REMARK 3 S TENSOR REMARK 3 S11: -0.2733 S12: -0.4100 S13: 0.7979 REMARK 3 S21: 0.9889 S22: -0.1740 S23: -0.9576 REMARK 3 S31: -1.3558 S32: 0.9174 S33: 0.3028 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 100:111) REMARK 3 ORIGIN FOR THE GROUP (A): 8.2646 -4.4684 -29.0574 REMARK 3 T TENSOR REMARK 3 T11: 0.2019 T22: 0.1901 REMARK 3 T33: 0.2379 T12: 0.0406 REMARK 3 T13: 0.0325 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 8.9284 L22: 7.6868 REMARK 3 L33: 2.4216 L12: 0.7812 REMARK 3 L13: 1.0114 L23: 2.1465 REMARK 3 S TENSOR REMARK 3 S11: -0.0713 S12: 0.4840 S13: -0.6392 REMARK 3 S21: -0.0212 S22: -0.3977 S23: -0.0473 REMARK 3 S31: 0.3013 S32: 0.3214 S33: 0.3821 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 112:128) REMARK 3 ORIGIN FOR THE GROUP (A): 6.8833 2.5381 -32.6595 REMARK 3 T TENSOR REMARK 3 T11: 0.1244 T22: 0.1608 REMARK 3 T33: 0.2008 T12: 0.0092 REMARK 3 T13: -0.0347 T23: 0.0661 REMARK 3 L TENSOR REMARK 3 L11: 8.3915 L22: 9.0052 REMARK 3 L33: 6.9422 L12: 4.4800 REMARK 3 L13: 1.7036 L23: 3.3297 REMARK 3 S TENSOR REMARK 3 S11: 0.0130 S12: 0.4125 S13: -0.4448 REMARK 3 S21: 0.0072 S22: -0.1676 S23: -0.6757 REMARK 3 S31: -0.1977 S32: 0.4065 S33: 0.1226 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 129:137) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9469 15.3179 -21.8688 REMARK 3 T TENSOR REMARK 3 T11: 0.8142 T22: 0.2009 REMARK 3 T33: 0.5548 T12: -0.5923 REMARK 3 T13: -0.4307 T23: 0.2128 REMARK 3 L TENSOR REMARK 3 L11: 1.0154 L22: 2.3351 REMARK 3 L33: 0.4514 L12: 1.3253 REMARK 3 L13: -0.2176 L23: 0.2121 REMARK 3 S TENSOR REMARK 3 S11: -0.0204 S12: -0.0704 S13: -0.0445 REMARK 3 S21: 0.2384 S22: -0.0525 S23: -0.2879 REMARK 3 S31: 0.0511 S32: 0.0958 S33: 0.0106 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN B AND RESID 1:30) REMARK 3 ORIGIN FOR THE GROUP (A): -17.0105 6.1720 -14.5263 REMARK 3 T TENSOR REMARK 3 T11: 0.1550 T22: 0.1871 REMARK 3 T33: 0.1365 T12: -0.0103 REMARK 3 T13: -0.0340 T23: -0.0246 REMARK 3 L TENSOR REMARK 3 L11: 1.4217 L22: 3.0556 REMARK 3 L33: 2.0351 L12: 0.3500 REMARK 3 L13: -0.8618 L23: -0.8266 REMARK 3 S TENSOR REMARK 3 S11: -0.0673 S12: -0.1449 S13: -0.1093 REMARK 3 S21: 0.1076 S22: 0.0805 S23: -0.2771 REMARK 3 S31: -0.0099 S32: 0.0793 S33: -0.0067 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN B AND RESID 31:39) REMARK 3 ORIGIN FOR THE GROUP (A): -26.9536 -8.0489 -13.0703 REMARK 3 T TENSOR REMARK 3 T11: 0.3052 T22: 0.3790 REMARK 3 T33: 0.3618 T12: -0.0141 REMARK 3 T13: -0.0504 T23: -0.0983 REMARK 3 L TENSOR REMARK 3 L11: 4.4689 L22: 2.2157 REMARK 3 L33: 5.2349 L12: -2.6645 REMARK 3 L13: 1.2609 L23: -2.4732 REMARK 3 S TENSOR REMARK 3 S11: 0.1020 S12: 0.8776 S13: -0.8041 REMARK 3 S21: -0.9468 S22: 0.0553 S23: 1.1963 REMARK 3 S31: 0.4408 S32: -0.0849 S33: -0.1181 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN B AND RESID 40:50) REMARK 3 ORIGIN FOR THE GROUP (A): -18.0756 -6.9201 -5.4864 REMARK 3 T TENSOR REMARK 3 T11: 0.2749 T22: 0.3924 REMARK 3 T33: 0.2740 T12: 0.0501 REMARK 3 T13: 0.0277 T23: 0.0998 REMARK 3 L TENSOR REMARK 3 L11: 4.9553 L22: 2.8480 REMARK 3 L33: 4.8867 L12: 1.7443 REMARK 3 L13: -4.8409 L23: -2.2925 REMARK 3 S TENSOR REMARK 3 S11: -0.1554 S12: -0.5312 S13: -0.6162 REMARK 3 S21: -0.0935 S22: -0.5005 S23: -0.6026 REMARK 3 S31: 0.7558 S32: 1.0357 S33: 0.7067 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN B AND RESID 51:60) REMARK 3 ORIGIN FOR THE GROUP (A): -14.9214 -2.9993 -17.5738 REMARK 3 T TENSOR REMARK 3 T11: 0.2158 T22: 0.2192 REMARK 3 T33: 0.2304 T12: -0.0145 REMARK 3 T13: 0.0384 T23: -0.0106 REMARK 3 L TENSOR REMARK 3 L11: 2.9504 L22: 9.7855 REMARK 3 L33: 4.1942 L12: -3.1552 REMARK 3 L13: 0.5588 L23: -5.7207 REMARK 3 S TENSOR REMARK 3 S11: -0.2356 S12: 0.0922 S13: -0.3126 REMARK 3 S21: -0.3006 S22: 0.0681 S23: -0.1469 REMARK 3 S31: 0.5301 S32: 0.0568 S33: 0.2563 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN B AND RESID 61:77) REMARK 3 ORIGIN FOR THE GROUP (A): -17.0469 10.5464 -28.8727 REMARK 3 T TENSOR REMARK 3 T11: 0.2176 T22: 0.1908 REMARK 3 T33: 0.1353 T12: -0.0226 REMARK 3 T13: 0.0236 T23: -0.0270 REMARK 3 L TENSOR REMARK 3 L11: 3.5811 L22: 8.3026 REMARK 3 L33: 4.5767 L12: -2.7962 REMARK 3 L13: 1.7073 L23: -4.8897 REMARK 3 S TENSOR REMARK 3 S11: 0.2675 S12: 0.2269 S13: 0.0170 REMARK 3 S21: -0.2954 S22: -0.1919 S23: -0.0255 REMARK 3 S31: -0.1706 S32: 0.3636 S33: -0.0994 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: (CHAIN B AND RESID 78:86) REMARK 3 ORIGIN FOR THE GROUP (A): -22.9904 0.2023 -33.2221 REMARK 3 T TENSOR REMARK 3 T11: 0.7642 T22: 0.3589 REMARK 3 T33: 0.5757 T12: 0.0581 REMARK 3 T13: -0.4818 T23: -0.0859 REMARK 3 L TENSOR REMARK 3 L11: 1.7209 L22: 0.1358 REMARK 3 L33: 3.2434 L12: -0.0280 REMARK 3 L13: 1.2100 L23: 0.5493 REMARK 3 S TENSOR REMARK 3 S11: 0.6446 S12: -0.1499 S13: -0.8858 REMARK 3 S21: 0.2519 S22: -0.0547 S23: -0.1574 REMARK 3 S31: 1.1713 S32: -0.1292 S33: -0.6013 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: (CHAIN B AND RESID 87:94) REMARK 3 ORIGIN FOR THE GROUP (A): -28.2731 -3.5664 -26.4243 REMARK 3 T TENSOR REMARK 3 T11: 0.9898 T22: 0.5646 REMARK 3 T33: 0.8756 T12: -0.1782 REMARK 3 T13: -0.0905 T23: -0.1679 REMARK 3 L TENSOR REMARK 3 L11: 5.9328 L22: 7.2310 REMARK 3 L33: 2.3392 L12: -4.6862 REMARK 3 L13: -3.3268 L23: 3.1073 REMARK 3 S TENSOR REMARK 3 S11: 0.1320 S12: 0.6916 S13: -1.4815 REMARK 3 S21: 0.1093 S22: -0.1506 S23: 0.5238 REMARK 3 S31: 0.8731 S32: -0.0581 S33: 0.2236 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: (CHAIN B AND RESID 95:111) REMARK 3 ORIGIN FOR THE GROUP (A): -25.3226 9.6107 -15.0943 REMARK 3 T TENSOR REMARK 3 T11: 0.2121 T22: 0.2015 REMARK 3 T33: 0.1311 T12: -0.0162 REMARK 3 T13: 0.0042 T23: 0.0364 REMARK 3 L TENSOR REMARK 3 L11: 8.4727 L22: 8.4023 REMARK 3 L33: 3.0590 L12: 5.5376 REMARK 3 L13: 4.1847 L23: 4.8791 REMARK 3 S TENSOR REMARK 3 S11: -0.1767 S12: -0.3259 S13: 0.1530 REMARK 3 S21: 0.0009 S22: 0.2554 S23: 0.3557 REMARK 3 S31: -0.0504 S32: -0.1452 S33: -0.0665 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: (CHAIN B AND RESID 112:128) REMARK 3 ORIGIN FOR THE GROUP (A): -22.3485 16.2954 -20.3017 REMARK 3 T TENSOR REMARK 3 T11: 0.1898 T22: 0.1933 REMARK 3 T33: 0.1398 T12: -0.0372 REMARK 3 T13: 0.0283 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 9.1496 L22: 5.4135 REMARK 3 L33: 6.5187 L12: 2.9568 REMARK 3 L13: 6.3512 L23: 3.7358 REMARK 3 S TENSOR REMARK 3 S11: -0.0452 S12: -0.3711 S13: 0.3486 REMARK 3 S21: -0.0328 S22: -0.0173 S23: 0.1883 REMARK 3 S31: -0.0962 S32: -0.4789 S33: 0.0360 REMARK 3 TLS GROUP : 20 REMARK 3 SELECTION: (CHAIN B AND RESID 129:137) REMARK 3 ORIGIN FOR THE GROUP (A): -30.8674 5.6438 -31.9179 REMARK 3 T TENSOR REMARK 3 T11: 0.5312 T22: 0.5019 REMARK 3 T33: 0.2980 T12: -0.1635 REMARK 3 T13: -0.1434 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 4.8705 L22: 3.9220 REMARK 3 L33: 8.9302 L12: -0.3526 REMARK 3 L13: 2.8720 L23: 4.9604 REMARK 3 S TENSOR REMARK 3 S11: 0.6709 S12: -0.4201 S13: -0.6558 REMARK 3 S21: 0.4959 S22: -0.5925 S23: 0.5243 REMARK 3 S31: 1.1240 S32: -1.5124 S33: 0.0140 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 6VDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246220. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30258 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 37.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 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: 3IXF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULPHATE MPEG 2000 29 REMARK 280 -33%, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 29.61350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.06600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.72850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.06600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.61350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.72850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 LYS A 36 CD CE NZ REMARK 470 GLN A 85 CD OE1 NE2 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 ARG A 122 NE CZ NH1 NH2 REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 ARG B 33 CG CD NE CZ NH1 REMARK 470 ASN B 34 CG OD1 ND2 REMARK 470 LYS B 51 CG CD CE NZ REMARK 470 LYS B 87 CG CD CE NZ REMARK 470 LYS B 125 CE NZ REMARK 470 LYS B 137 CG CD CE NZ 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 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 122 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 122 NE - CZ - NH2 ANGL. DEV. = -3.5 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 ASP A 12 51.06 -147.94 REMARK 500 ASN B 34 2.90 -169.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 HEM A 201 REMARK 610 HEM B 402 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 NE2 REMARK 620 2 HEM A 201 NA 74.5 REMARK 620 3 HEM A 201 NB 92.8 90.8 REMARK 620 4 HEM A 201 NC 103.6 178.1 89.5 REMARK 620 5 HEM A 201 ND 89.2 88.8 177.7 91.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 89 NE2 REMARK 620 2 HEM B 402 NA 70.8 REMARK 620 3 HEM B 402 NB 92.3 93.5 REMARK 620 4 HEM B 402 NC 106.0 176.8 87.0 REMARK 620 5 HEM B 402 ND 90.9 90.5 175.5 89.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue T6C A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue T6C B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 405 DBREF 6VDY A 1 137 UNP Q9NAV7 Q9NAV7_9ANNE 2 138 DBREF 6VDY B 1 137 UNP Q9NAV7 Q9NAV7_9ANNE 2 138 SEQRES 1 A 137 GLY PHE LYS GLN ASP ILE ALA THR LEU ARG GLY ASP LEU SEQRES 2 A 137 ARG THR TYR ALA GLN ASP ILE PHE LEU ALA PHE LEU ASN SEQRES 3 A 137 LYS TYR PRO ASP GLU LYS ARG ASN PHE LYS ASN TYR VAL SEQRES 4 A 137 GLY LYS SER ASP GLN GLU LEU LYS SER MET ALA LYS PHE SEQRES 5 A 137 GLY ASP HIS THR GLU LYS VAL PHE ASN LEU MET MET GLU SEQRES 6 A 137 VAL ALA ASP ARG ALA THR ASP CYS VAL PRO LEU ALA SER SEQRES 7 A 137 ASP ALA SER THR LEU VAL GLN MET LYS GLN HIS SER GLY SEQRES 8 A 137 LEU THR THR GLY ASN PHE GLU LYS LEU PHE VAL ALA LEU SEQRES 9 A 137 VAL GLU TYR MET ARG ALA SER GLY GLN SER PHE ASP SER SEQRES 10 A 137 GLN SER TRP ASP ARG PHE GLY LYS ASN LEU VAL SER ALA SEQRES 11 A 137 LEU SER SER ALA GLY MET LYS SEQRES 1 B 137 GLY PHE LYS GLN ASP ILE ALA THR LEU ARG GLY ASP LEU SEQRES 2 B 137 ARG THR TYR ALA GLN ASP ILE PHE LEU ALA PHE LEU ASN SEQRES 3 B 137 LYS TYR PRO ASP GLU LYS ARG ASN PHE LYS ASN TYR VAL SEQRES 4 B 137 GLY LYS SER ASP GLN GLU LEU LYS SER MET ALA LYS PHE SEQRES 5 B 137 GLY ASP HIS THR GLU LYS VAL PHE ASN LEU MET MET GLU SEQRES 6 B 137 VAL ALA ASP ARG ALA THR ASP CYS VAL PRO LEU ALA SER SEQRES 7 B 137 ASP ALA SER THR LEU VAL GLN MET LYS GLN HIS SER GLY SEQRES 8 B 137 LEU THR THR GLY ASN PHE GLU LYS LEU PHE VAL ALA LEU SEQRES 9 B 137 VAL GLU TYR MET ARG ALA SER GLY GLN SER PHE ASP SER SEQRES 10 B 137 GLN SER TRP ASP ARG PHE GLY LYS ASN LEU VAL SER ALA SEQRES 11 B 137 LEU SER SER ALA GLY MET LYS HET HEM A 201 39 HET T6C A 202 10 HET EDO A 203 4 HET SO4 A 204 5 HET SO4 A 205 5 HET EDO B 401 4 HET HEM B 402 39 HET T6C B 403 10 HET EDO B 404 4 HET EDO B 405 4 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM T6C 2,4,6-TRICHLOROPHENOL HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN HEM HEME HETSYN EDO ETHYLENE GLYCOL FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 T6C 2(C6 H3 CL3 O) FORMUL 5 EDO 4(C2 H6 O2) FORMUL 6 SO4 2(O4 S 2-) FORMUL 13 HOH *166(H2 O) HELIX 1 AA1 GLY A 1 GLY A 11 1 11 HELIX 2 AA2 ASP A 12 TYR A 28 1 17 HELIX 3 AA3 PRO A 29 VAL A 39 5 11 HELIX 4 AA4 SER A 42 LYS A 47 1 6 HELIX 5 AA5 MET A 49 ALA A 70 1 22 HELIX 6 AA6 LEU A 76 GLN A 85 1 10 HELIX 7 AA7 MET A 86 SER A 90 5 5 HELIX 8 AA8 THR A 93 SER A 111 1 19 HELIX 9 AA9 ASP A 116 ALA A 134 1 19 HELIX 10 AB1 PHE B 2 ASP B 12 1 11 HELIX 11 AB2 ASP B 12 TYR B 28 1 17 HELIX 12 AB3 PHE B 35 VAL B 39 5 5 HELIX 13 AB4 SER B 42 LYS B 47 1 6 HELIX 14 AB5 MET B 49 ALA B 70 1 22 HELIX 15 AB6 LEU B 76 GLN B 85 1 10 HELIX 16 AB7 MET B 86 SER B 90 5 5 HELIX 17 AB8 THR B 93 SER B 111 1 19 HELIX 18 AB9 ASP B 116 ALA B 134 1 19 LINK NE2 HIS A 89 FE HEM A 201 1555 1555 2.39 LINK NE2 HIS B 89 FE HEM B 402 1555 1555 2.56 SITE 1 AC1 17 PHE A 24 GLU A 31 HIS A 55 LYS A 58 SITE 2 AC1 17 VAL A 59 LEU A 62 MET A 63 LEU A 83 SITE 3 AC1 17 MET A 86 GLN A 88 HIS A 89 LEU A 92 SITE 4 AC1 17 ASN A 96 PHE A 97 LEU A 100 LEU A 127 SITE 5 AC1 17 T6C A 202 SITE 1 AC2 8 PHE A 21 PHE A 35 TYR A 38 PHE A 52 SITE 2 AC2 8 HIS A 55 THR A 56 VAL A 59 HEM A 201 SITE 1 AC3 6 GLN A 4 ASP A 5 THR A 8 SER A 114 SITE 2 AC3 6 HOH A 309 HOH B 521 SITE 1 AC4 9 GLY A 1 PHE A 2 LYS A 3 ASP A 116 SITE 2 AC4 9 HOH A 311 HOH A 363 HOH A 368 LYS B 32 SITE 3 AC4 9 GLY B 40 SITE 1 AC5 10 LYS A 32 VAL A 39 GLY A 40 HOH A 312 SITE 2 AC5 10 HOH A 320 HOH A 356 GLY B 1 PHE B 2 SITE 3 AC5 10 LYS B 3 HOH B 561 SITE 1 AC6 6 GLU A 45 ASP A 68 ARG A 69 HOH A 339 SITE 2 AC6 6 ASP B 68 HOH B 537 SITE 1 AC7 17 PHE B 24 GLU B 31 PHE B 35 HIS B 55 SITE 2 AC7 17 LYS B 58 VAL B 59 LEU B 62 MET B 63 SITE 3 AC7 17 LEU B 83 MET B 86 GLN B 88 HIS B 89 SITE 4 AC7 17 LEU B 92 ASN B 96 PHE B 97 LEU B 127 SITE 5 AC7 17 T6C B 403 SITE 1 AC8 7 PHE B 21 PHE B 35 TYR B 38 HIS B 55 SITE 2 AC8 7 THR B 56 VAL B 59 HEM B 402 SITE 1 AC9 5 HOH A 317 ASP B 5 THR B 8 SER B 114 SITE 2 AC9 5 HOH B 534 SITE 1 AD1 7 THR A 71 PRO B 75 ASN B 126 SER B 129 SITE 2 AD1 7 ALA B 130 HOH B 502 HOH B 542 CRYST1 59.227 67.457 68.132 90.00 90.00 90.00 P 21 21 21 8 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 0.016884 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014824 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014677 0.00000