HEADER OXIDOREDUCTASE 14-FEB-23 8CK9 TITLE DYP-TYPE PEROXIDASE FROM THERMOBIFIDA HALOTOLERANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE MODEL CONTAINS BOUND HEME (HEM) AND NITRATE (NO3) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOBIFIDA HALOTOLERANS; SOURCE 3 ORGANISM_TAXID: 483545; SOURCE 4 GENE: NI17_20570; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEME, PEROXIDASE, DYP, FERREDOXIN-LIKE FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.PUPART,T.LUKK REVDAT 2 06-MAR-24 8CK9 1 JRNL REVDAT 1 28-FEB-24 8CK9 0 JRNL AUTH H.PUPART,T.LUKK,P.VALJAMAE JRNL TITL DYE-DECOLORIZING PEROXIDASE OF THERMOBIFIDA HALOTOLERANCE JRNL TITL 2 DISPLAYS COMPLEX KINETICS WITH BOTH SUBSTRATE INHIBITION AND JRNL TITL 3 APPARENT POSITIVE COOPERATIVITY. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 754 09931 2024 JRNL REFN ESSN 1096-0384 JRNL PMID 38382807 JRNL DOI 10.1016/J.ABB.2024.109931 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 49628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2473 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 29.6100 - 4.1900 1.00 2795 134 0.1551 0.1902 REMARK 3 2 4.1900 - 3.3300 1.00 2653 162 0.1410 0.1681 REMARK 3 3 3.3300 - 2.9100 1.00 2672 124 0.1642 0.1915 REMARK 3 4 2.9100 - 2.6400 1.00 2653 118 0.1692 0.1980 REMARK 3 5 2.6400 - 2.4500 1.00 2650 134 0.1629 0.1756 REMARK 3 6 2.4500 - 2.3100 1.00 2610 145 0.1585 0.2065 REMARK 3 7 2.3100 - 2.1900 1.00 2603 143 0.1577 0.1982 REMARK 3 8 2.1900 - 2.1000 0.99 2605 145 0.1565 0.1576 REMARK 3 9 2.1000 - 2.0200 1.00 2600 146 0.1540 0.1936 REMARK 3 10 2.0200 - 1.9500 1.00 2594 121 0.1550 0.1765 REMARK 3 11 1.9500 - 1.8900 1.00 2618 133 0.1510 0.1791 REMARK 3 12 1.8900 - 1.8300 1.00 2619 145 0.1559 0.2042 REMARK 3 13 1.8300 - 1.7800 1.00 2581 147 0.1617 0.2167 REMARK 3 14 1.7800 - 1.7400 1.00 2609 123 0.1652 0.2036 REMARK 3 15 1.7400 - 1.7000 0.99 2545 141 0.1562 0.1857 REMARK 3 16 1.7000 - 1.6600 1.00 2620 131 0.1625 0.2084 REMARK 3 17 1.6600 - 1.6300 1.00 2561 149 0.1596 0.2007 REMARK 3 18 1.6300 - 1.6000 1.00 2567 132 0.1665 0.1976 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 2983 REMARK 3 ANGLE : 0.829 4081 REMARK 3 CHIRALITY : 0.050 438 REMARK 3 PLANARITY : 0.008 553 REMARK 3 DIHEDRAL : 12.779 1091 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.1356 2.8995 -22.0577 REMARK 3 T TENSOR REMARK 3 T11: 0.3535 T22: 0.1548 REMARK 3 T33: 0.2234 T12: 0.0289 REMARK 3 T13: 0.0134 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.0974 L22: 0.0713 REMARK 3 L33: 0.1623 L12: 0.0878 REMARK 3 L13: 0.1278 L23: 0.1190 REMARK 3 S TENSOR REMARK 3 S11: 0.0507 S12: 0.0650 S13: -0.1459 REMARK 3 S21: -0.0819 S22: -0.0397 S23: -0.0742 REMARK 3 S31: 0.4299 S32: 0.0062 S33: -0.0037 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 37 THROUGH 61 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.8409 24.2246 -16.9219 REMARK 3 T TENSOR REMARK 3 T11: 0.1177 T22: 0.0724 REMARK 3 T33: 0.1175 T12: 0.0291 REMARK 3 T13: 0.0029 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.2284 L22: 0.0525 REMARK 3 L33: 0.1383 L12: 0.0993 REMARK 3 L13: -0.0060 L23: 0.0409 REMARK 3 S TENSOR REMARK 3 S11: -0.0507 S12: 0.0122 S13: 0.0551 REMARK 3 S21: -0.0006 S22: 0.0351 S23: 0.0106 REMARK 3 S31: -0.0017 S32: -0.0186 S33: -0.0082 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 62 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0176 20.7648 -10.8603 REMARK 3 T TENSOR REMARK 3 T11: 0.1383 T22: 0.0965 REMARK 3 T33: 0.1491 T12: -0.0130 REMARK 3 T13: 0.0153 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.1024 L22: 0.1359 REMARK 3 L33: 0.1582 L12: -0.0355 REMARK 3 L13: 0.0930 L23: -0.1034 REMARK 3 S TENSOR REMARK 3 S11: 0.0059 S12: -0.0500 S13: 0.0114 REMARK 3 S21: 0.0916 S22: -0.1509 S23: 0.0776 REMARK 3 S31: 0.1783 S32: -0.2128 S33: -0.0064 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 87 THROUGH 126 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9142 20.6067 -13.3465 REMARK 3 T TENSOR REMARK 3 T11: 0.0862 T22: 0.0872 REMARK 3 T33: 0.1081 T12: 0.0097 REMARK 3 T13: -0.0011 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.2081 L22: 0.1579 REMARK 3 L33: 0.2762 L12: -0.1500 REMARK 3 L13: -0.0475 L23: -0.0985 REMARK 3 S TENSOR REMARK 3 S11: -0.0440 S12: -0.0419 S13: 0.0003 REMARK 3 S21: 0.0264 S22: 0.0394 S23: 0.0379 REMARK 3 S31: 0.0363 S32: -0.0085 S33: -0.0014 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 127 THROUGH 154 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.0317 29.1660 -19.0137 REMARK 3 T TENSOR REMARK 3 T11: 0.1117 T22: 0.0646 REMARK 3 T33: 0.1210 T12: 0.0034 REMARK 3 T13: 0.0012 T23: 0.0182 REMARK 3 L TENSOR REMARK 3 L11: 0.2256 L22: 0.1234 REMARK 3 L33: 0.1293 L12: -0.0649 REMARK 3 L13: -0.0411 L23: 0.0162 REMARK 3 S TENSOR REMARK 3 S11: -0.0348 S12: 0.0726 S13: 0.0818 REMARK 3 S21: -0.0836 S22: -0.0017 S23: -0.0020 REMARK 3 S31: -0.0504 S32: -0.0070 S33: -0.0221 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 155 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.8398 23.8744 -23.2295 REMARK 3 T TENSOR REMARK 3 T11: 0.1218 T22: 0.1106 REMARK 3 T33: 0.1359 T12: 0.0179 REMARK 3 T13: -0.0173 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.1048 L22: 0.0548 REMARK 3 L33: 0.1211 L12: 0.0270 REMARK 3 L13: 0.1169 L23: 0.0240 REMARK 3 S TENSOR REMARK 3 S11: -0.0417 S12: 0.0654 S13: 0.0525 REMARK 3 S21: -0.1272 S22: -0.0125 S23: 0.0517 REMARK 3 S31: -0.0125 S32: -0.0743 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 183 THROUGH 220 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.4143 8.9750 -22.4006 REMARK 3 T TENSOR REMARK 3 T11: 0.1485 T22: 0.1295 REMARK 3 T33: 0.1737 T12: 0.0232 REMARK 3 T13: 0.0110 T23: 0.0582 REMARK 3 L TENSOR REMARK 3 L11: 0.1887 L22: 0.0274 REMARK 3 L33: 0.1416 L12: 0.0004 REMARK 3 L13: 0.0723 L23: 0.0667 REMARK 3 S TENSOR REMARK 3 S11: -0.0736 S12: -0.0456 S13: -0.2555 REMARK 3 S21: -0.0405 S22: 0.1330 S23: 0.0311 REMARK 3 S31: 0.1051 S32: 0.0039 S33: 0.0138 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 221 THROUGH 246 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.1218 22.1357 -6.9243 REMARK 3 T TENSOR REMARK 3 T11: 0.0912 T22: 0.1214 REMARK 3 T33: 0.0812 T12: 0.0223 REMARK 3 T13: 0.0116 T23: 0.0370 REMARK 3 L TENSOR REMARK 3 L11: 0.2944 L22: 0.1509 REMARK 3 L33: 0.0713 L12: 0.0999 REMARK 3 L13: 0.0131 L23: 0.0990 REMARK 3 S TENSOR REMARK 3 S11: -0.0558 S12: -0.1418 S13: 0.0320 REMARK 3 S21: 0.0246 S22: -0.0437 S23: -0.0297 REMARK 3 S31: 0.0610 S32: 0.1356 S33: -0.0259 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 247 THROUGH 283 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.3939 14.9660 -30.4894 REMARK 3 T TENSOR REMARK 3 T11: 0.1063 T22: 0.1859 REMARK 3 T33: 0.0991 T12: -0.0056 REMARK 3 T13: 0.0151 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 0.2655 L22: 0.2608 REMARK 3 L33: 0.2121 L12: 0.2066 REMARK 3 L13: 0.0509 L23: 0.1917 REMARK 3 S TENSOR REMARK 3 S11: -0.0287 S12: 0.2562 S13: -0.0869 REMARK 3 S21: -0.0951 S22: 0.0744 S23: -0.0300 REMARK 3 S31: 0.0305 S32: 0.1560 S33: 0.0078 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 284 THROUGH 308 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.7590 18.1794 -19.8977 REMARK 3 T TENSOR REMARK 3 T11: 0.0733 T22: 0.1756 REMARK 3 T33: 0.0832 T12: 0.0011 REMARK 3 T13: 0.0033 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.0562 L22: 0.0268 REMARK 3 L33: 0.0859 L12: -0.0477 REMARK 3 L13: 0.0223 L23: -0.0125 REMARK 3 S TENSOR REMARK 3 S11: -0.0564 S12: -0.1352 S13: 0.0908 REMARK 3 S21: 0.0417 S22: 0.0499 S23: -0.0334 REMARK 3 S31: -0.0433 S32: 0.2223 S33: -0.0016 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 309 THROUGH 332 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.3157 23.8764 -26.2175 REMARK 3 T TENSOR REMARK 3 T11: 0.1431 T22: 0.1187 REMARK 3 T33: 0.0984 T12: -0.0260 REMARK 3 T13: -0.0173 T23: 0.0480 REMARK 3 L TENSOR REMARK 3 L11: 0.2469 L22: 0.1291 REMARK 3 L33: 0.1721 L12: 0.0609 REMARK 3 L13: -0.0557 L23: 0.1398 REMARK 3 S TENSOR REMARK 3 S11: -0.1038 S12: 0.0917 S13: 0.0232 REMARK 3 S21: -0.0803 S22: 0.0431 S23: 0.0055 REMARK 3 S31: -0.1729 S32: 0.1146 S33: -0.0088 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 333 THROUGH 360 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.1239 24.4507 -15.2967 REMARK 3 T TENSOR REMARK 3 T11: 0.0943 T22: 0.1179 REMARK 3 T33: 0.0972 T12: -0.0094 REMARK 3 T13: 0.0025 T23: 0.0203 REMARK 3 L TENSOR REMARK 3 L11: 0.1121 L22: 0.1026 REMARK 3 L33: 0.0675 L12: -0.0401 REMARK 3 L13: -0.0881 L23: 0.0387 REMARK 3 S TENSOR REMARK 3 S11: -0.0430 S12: -0.0855 S13: 0.0773 REMARK 3 S21: 0.0304 S22: 0.0473 S23: 0.0219 REMARK 3 S31: -0.0930 S32: 0.0491 S33: 0.0179 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 361 THROUGH 391 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.5371 23.4884 -12.7328 REMARK 3 T TENSOR REMARK 3 T11: 0.0879 T22: 0.0847 REMARK 3 T33: 0.0812 T12: -0.0007 REMARK 3 T13: 0.0171 T23: 0.0352 REMARK 3 L TENSOR REMARK 3 L11: 0.2897 L22: 0.1639 REMARK 3 L33: 0.2629 L12: 0.0846 REMARK 3 L13: 0.2201 L23: 0.1889 REMARK 3 S TENSOR REMARK 3 S11: 0.0210 S12: -0.0580 S13: 0.1028 REMARK 3 S21: 0.0210 S22: 0.0005 S23: 0.0257 REMARK 3 S31: 0.0042 S32: -0.0434 S33: -0.0240 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 8CK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128649. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.97926 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49674 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.27700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION WAS AT 15 MG/ML REMARK 280 IN TRIS-HCL (20 MM, PH 7.5); MOTHER LIQUOR WAS 0.2 M SODIUM REMARK 280 NITRATE, 0.1 M BIS-TRIS PROPANE, PH 7.5, 20% (W/V) PEG3350., REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 282K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.82450 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 67.82450 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 1.000000 0.000000 0.000000 35.17900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.18500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.17900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.18500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.82450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.17900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.18500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.82450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.17900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.18500 REMARK 290 SMTRY3 8 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: 7130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -67.82450 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 862 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 872 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 896 LIES ON A SPECIAL POSITION. 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 -35 REMARK 465 THR A -34 REMARK 465 GLY A -33 REMARK 465 PRO A -32 REMARK 465 GLU A -31 REMARK 465 PRO A -30 REMARK 465 THR A -29 REMARK 465 ARG A -28 REMARK 465 THR A -27 REMARK 465 GLY A -26 REMARK 465 ASN A -25 REMARK 465 ALA A -24 REMARK 465 SER A -23 REMARK 465 ARG A -22 REMARK 465 ARG A -21 REMARK 465 ARG A -20 REMARK 465 PHE A -19 REMARK 465 LEU A -18 REMARK 465 ALA A -17 REMARK 465 GLY A -16 REMARK 465 LEU A -15 REMARK 465 GLY A -14 REMARK 465 ALA A -13 REMARK 465 ALA A -12 REMARK 465 ALA A -11 REMARK 465 LEU A -10 REMARK 465 THR A -9 REMARK 465 GLY A -8 REMARK 465 ALA A -7 REMARK 465 GLY A -6 REMARK 465 ALA A -5 REMARK 465 GLY A -4 REMARK 465 MET A -3 REMARK 465 ALA A -2 REMARK 465 ALA A -1 REMARK 465 GLY A 0 REMARK 465 GLU A 1 REMARK 465 ALA A 2 REMARK 465 VAL A 3 REMARK 465 ARG A 4 REMARK 465 PRO A 5 REMARK 465 LEU A 6 REMARK 465 LEU A 7 REMARK 465 PRO A 8 REMARK 465 ASP A 9 REMARK 465 PRO A 10 REMARK 465 GLY A 11 REMARK 465 PRO A 12 REMARK 465 ALA A 13 REMARK 465 THR A 14 REMARK 465 ASP A 15 REMARK 465 PRO A 16 REMARK 465 ALA A 17 REMARK 465 GLY A 392 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 ILE A 39 -59.99 -123.54 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 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 300 NE2 REMARK 620 2 HEM A 401 NA 91.7 REMARK 620 3 HEM A 401 NB 92.8 91.1 REMARK 620 4 HEM A 401 NC 94.8 173.4 89.3 REMARK 620 5 HEM A 401 ND 93.2 88.9 174.0 90.0 REMARK 620 6 NO3 A 402 O2 172.6 85.1 80.6 88.5 93.5 REMARK 620 N 1 2 3 4 5 DBREF1 8CK9 A -35 392 UNP A0A399FZ67_9ACTN DBREF2 8CK9 A A0A399FZ67 1 428 SEQRES 1 A 428 MET THR GLY PRO GLU PRO THR ARG THR GLY ASN ALA SER SEQRES 2 A 428 ARG ARG ARG PHE LEU ALA GLY LEU GLY ALA ALA ALA LEU SEQRES 3 A 428 THR GLY ALA GLY ALA GLY MET ALA ALA GLY GLU ALA VAL SEQRES 4 A 428 ARG PRO LEU LEU PRO ASP PRO GLY PRO ALA THR ASP PRO SEQRES 5 A 428 ALA ALA GLU GLU ARG LEU ARG MET ALA GLY GLN PRO ALA SEQRES 6 A 428 ASP ALA ALA ALA THR PRO GLN PRO GLY ILE THR GLY ARG SEQRES 7 A 428 ALA PRO ALA PHE VAL HIS VAL LEU SER PHE ASP LEU ALA SEQRES 8 A 428 ASP THR VAL ARG GLU ASN THR GLY THR ALA ARG GLU ALA SEQRES 9 A 428 ALA ALA THR VAL LEU ARG SER TRP ALA GLU LEU ALA THR SEQRES 10 A 428 ARG LEU HIS GLU ASP GLY PRO ALA GLU GLY THR ALA ALA SEQRES 11 A 428 THR GLY LEU LEU PRO ALA SER LEU MET VAL THR VAL GLY SEQRES 12 A 428 LEU GLY GLY SER LEU LEU GLN ALA ILE GLY ALA ALA ASP SEQRES 13 A 428 ARG ARG PRO ASP ALA LEU ALA ASP LEU PRO GLU PHE SER SEQRES 14 A 428 THR ASP GLU LEU ARG PRO ARG TRP CYS GLY GLY ASP LEU SEQRES 15 A 428 LEU LEU GLN ILE GLY ALA GLU ASP PRO MET VAL LEU ALA SEQRES 16 A 428 ALA ALA ALA ASP GLU LEU VAL ALA ALA SER THR ARG THR SEQRES 17 A 428 THR THR VAL ARG TRP ALA LEU ARG GLY PHE ARG HIS THR SEQRES 18 A 428 ALA ALA ALA ALA ARG ASN PRO ASP ALA THR PRO ARG ASN SEQRES 19 A 428 LEU MET GLY GLN ILE ASP GLY THR ALA ASN PRO ALA GLN SEQRES 20 A 428 ASP HIS ALA LEU PHE ASP ARG THR VAL THR ALA ARG GLU SEQRES 21 A 428 ALA ARG ASP PRO ALA HIS ALA TRP MET ASP GLY GLY SER SEQRES 22 A 428 TYR LEU VAL ILE ARG ARG ILE ARG MET LEU LEU ASP GLU SEQRES 23 A 428 TRP ARG GLY LEU ASP VAL PRO ALA ARG GLU ARG VAL LEU SEQRES 24 A 428 GLY ARG ARG LEU ASP THR GLY ALA PRO LEU GLY GLY ARG SEQRES 25 A 428 LYS GLU THR ASP PRO VAL VAL LEU THR ALA ARG ASP ALA SEQRES 26 A 428 SER GLY ARG PRO VAL ILE PRO GLU ASP ALA HIS VAL ARG SEQRES 27 A 428 LEU ALA ASN PRO GLU SER ASN LEU GLY ALA ARG MET PHE SEQRES 28 A 428 ARG ARG GLY TYR SER TYR ASP GLU GLY TRP ARG ASP ASP SEQRES 29 A 428 GLY VAL ARG ASP ALA GLY LEU LEU PHE MET ALA TRP GLN SEQRES 30 A 428 GLY ASP PRO ALA THR GLY PHE VAL PRO VAL GLN ARG SER SEQRES 31 A 428 LEU ALA ASP ARG GLY ASP ALA LEU ASN ARG TYR THR ARG SEQRES 32 A 428 HIS GLU GLY SER ALA LEU PHE ALA VAL PRO ALA ALA ALA SEQRES 33 A 428 ARG GLY ARG TYR PRO GLY GLN ASP LEU VAL GLU GLY HET HEM A 401 43 HET NO3 A 402 4 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NO3 NITRATE ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 NO3 N O3 1- FORMUL 4 HOH *423(H2 O) HELIX 1 AA1 ALA A 18 GLN A 27 1 10 HELIX 2 AA2 ASP A 56 ARG A 59 5 4 HELIX 3 AA3 ASN A 61 GLY A 87 1 27 HELIX 4 AA4 GLY A 109 ILE A 116 1 8 HELIX 5 AA5 ALA A 118 ARG A 122 5 5 HELIX 6 AA6 PRO A 123 ALA A 127 5 5 HELIX 7 AA7 ARG A 138 CYS A 142 5 5 HELIX 8 AA8 ASP A 154 ALA A 168 1 15 HELIX 9 AA9 THR A 185 ALA A 189 5 5 HELIX 10 AB1 HIS A 213 THR A 221 1 9 HELIX 11 AB2 ASP A 227 ASP A 234 5 8 HELIX 12 AB3 LEU A 247 GLY A 253 1 7 HELIX 13 AB4 ASP A 255 GLY A 264 1 10 HELIX 14 AB5 ALA A 299 ASN A 305 1 7 HELIX 15 AB6 PRO A 306 ASN A 309 5 4 HELIX 16 AB7 ASP A 343 THR A 346 5 4 HELIX 17 AB8 GLY A 347 ARG A 358 1 12 HELIX 18 AB9 ASP A 360 ARG A 364 5 5 HELIX 19 AC1 GLY A 386 GLU A 391 1 6 SHEET 1 AA1 4 MET A 103 LEU A 108 0 SHEET 2 AA1 4 LEU A 146 ALA A 152 -1 O GLY A 151 N MET A 103 SHEET 3 AA1 4 PHE A 46 LEU A 54 -1 N PHE A 52 O LEU A 146 SHEET 4 AA1 4 THR A 173 PHE A 182 -1 O ARG A 176 N SER A 51 SHEET 1 AA2 3 PHE A 315 ARG A 316 0 SHEET 2 AA2 3 ARG A 331 GLN A 341 -1 O TRP A 340 N PHE A 315 SHEET 3 AA2 3 TYR A 319 TRP A 325 -1 N TYR A 319 O LEU A 336 SHEET 1 AA3 4 PHE A 315 ARG A 316 0 SHEET 2 AA3 4 ARG A 331 GLN A 341 -1 O TRP A 340 N PHE A 315 SHEET 3 AA3 4 SER A 237 MET A 246 -1 N VAL A 240 O ALA A 339 SHEET 4 AA3 4 THR A 366 VAL A 376 -1 O GLU A 369 N ARG A 243 LINK NE2 HIS A 300 FE HEM A 401 1555 1555 2.07 LINK FE HEM A 401 O2 NO3 A 402 1555 1555 2.39 CISPEP 1 THR A 34 PRO A 35 0 -3.69 CRYST1 70.358 78.370 135.649 90.00 90.00 90.00 C 2 2 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 0.014213 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012760 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007372 0.00000