HEADER HYDROLASE 19-AUG-13 4MB7 TITLE CRYSTAL STRUCTURE OF A VIRAL DNA GLYCOSYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE 8-LIKE L720; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENDONUCLEASE VIII-LIKE L720; COMPND 5 EC: 4.2.99.18, 3.2.2.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACANTHAMOEBA POLYPHAGA MIMIVIRUS; SOURCE 3 ORGANISM_COMMON: APMV; SOURCE 4 ORGANISM_TAXID: 212035; SOURCE 5 GENE: ENDONUCLEASE VIII (NEI) 2, MIMI_L720; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE3) PLYS S; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETDUET-1 KEYWDS ZINC-FINGER DOMAIN, H2TH-MOTIF, DNA GLYCOSYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.PRAKASH,B.E.ECKENROTH,S.DOUBLIE REVDAT 3 28-FEB-24 4MB7 1 REMARK LINK REVDAT 2 11-DEC-13 4MB7 1 JRNL REVDAT 1 30-OCT-13 4MB7 0 JRNL AUTH A.PRAKASH,B.E.ECKENROTH,A.M.AVERILL,K.IMAMURA,S.S.WALLACE, JRNL AUTH 2 S.DOUBLIE JRNL TITL STRUCTURAL INVESTIGATION OF A VIRAL ORTHOLOG OF HUMAN JRNL TITL 2 NEIL2/3 DNA GLYCOSYLASES. JRNL REF DNA REPAIR V. 12 1062 2013 JRNL REFN ISSN 1568-7864 JRNL PMID 24120312 JRNL DOI 10.1016/J.DNAREP.2013.09.004 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29953 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.160 REMARK 3 FREE R VALUE TEST SET COUNT : 3043 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 38.7104 - 5.7105 1.00 1309 147 0.2138 0.2723 REMARK 3 2 5.7105 - 4.5348 1.00 1248 141 0.1590 0.1990 REMARK 3 3 4.5348 - 3.9622 1.00 1246 136 0.1542 0.1586 REMARK 3 4 3.9622 - 3.6003 1.00 1235 139 0.1680 0.2137 REMARK 3 5 3.6003 - 3.3424 1.00 1230 135 0.1728 0.2026 REMARK 3 6 3.3424 - 3.1454 1.00 1230 139 0.1885 0.1998 REMARK 3 7 3.1454 - 2.9879 1.00 1208 151 0.1915 0.2270 REMARK 3 8 2.9879 - 2.8579 1.00 1239 137 0.2037 0.2602 REMARK 3 9 2.8579 - 2.7479 1.00 1214 137 0.2096 0.2785 REMARK 3 10 2.7479 - 2.6531 1.00 1198 135 0.2006 0.2328 REMARK 3 11 2.6531 - 2.5702 1.00 1250 127 0.1855 0.2206 REMARK 3 12 2.5702 - 2.4967 1.00 1227 125 0.1821 0.2350 REMARK 3 13 2.4967 - 2.4310 1.00 1202 147 0.1864 0.2424 REMARK 3 14 2.4310 - 2.3717 1.00 1209 136 0.1957 0.2413 REMARK 3 15 2.3717 - 2.3178 1.00 1211 125 0.1894 0.2267 REMARK 3 16 2.3178 - 2.2685 1.00 1221 145 0.1910 0.2225 REMARK 3 17 2.2685 - 2.2231 1.00 1192 136 0.2010 0.2468 REMARK 3 18 2.2231 - 2.1812 1.00 1218 138 0.1920 0.2340 REMARK 3 19 2.1812 - 2.1422 1.00 1199 155 0.1887 0.2538 REMARK 3 20 2.1422 - 2.1059 1.00 1204 127 0.1981 0.2388 REMARK 3 21 2.1059 - 2.0719 1.00 1210 126 0.2182 0.3088 REMARK 3 22 2.0719 - 2.0400 1.00 1210 159 0.2350 0.2840 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.37 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 : 0.005 2317 REMARK 3 ANGLE : 0.916 3145 REMARK 3 CHIRALITY : 0.056 351 REMARK 3 PLANARITY : 0.004 390 REMARK 3 DIHEDRAL : 11.264 876 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 2 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3919 47.0795 60.8241 REMARK 3 T TENSOR REMARK 3 T11: 0.2106 T22: 0.1756 REMARK 3 T33: 0.2197 T12: 0.0471 REMARK 3 T13: 0.0012 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.0184 L22: 0.0015 REMARK 3 L33: 0.0105 L12: -0.0007 REMARK 3 L13: 0.0131 L23: 0.0004 REMARK 3 S TENSOR REMARK 3 S11: 0.1108 S12: -0.0629 S13: -0.1123 REMARK 3 S21: 0.0013 S22: 0.0787 S23: -0.0747 REMARK 3 S31: 0.0592 S32: 0.0293 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6480 60.3651 48.3611 REMARK 3 T TENSOR REMARK 3 T11: 0.1900 T22: 0.1920 REMARK 3 T33: 0.2213 T12: 0.0275 REMARK 3 T13: 0.0400 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 0.0270 L22: 0.1879 REMARK 3 L33: 0.1131 L12: 0.0188 REMARK 3 L13: 0.0377 L23: 0.1329 REMARK 3 S TENSOR REMARK 3 S11: -0.0610 S12: 0.0470 S13: 0.2267 REMARK 3 S21: -0.2451 S22: -0.0437 S23: 0.0560 REMARK 3 S31: -0.0075 S32: -0.0078 S33: -0.0279 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7348 60.1573 58.3041 REMARK 3 T TENSOR REMARK 3 T11: 0.1736 T22: 0.1379 REMARK 3 T33: 0.1791 T12: -0.0000 REMARK 3 T13: 0.0246 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 0.0419 L22: 0.0466 REMARK 3 L33: 0.0370 L12: -0.0302 REMARK 3 L13: 0.0228 L23: 0.0349 REMARK 3 S TENSOR REMARK 3 S11: -0.0329 S12: 0.0367 S13: 0.0568 REMARK 3 S21: -0.0383 S22: 0.0306 S23: -0.0699 REMARK 3 S31: 0.0132 S32: -0.0652 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.3614 45.2948 53.2172 REMARK 3 T TENSOR REMARK 3 T11: 0.2860 T22: 0.2467 REMARK 3 T33: 0.2398 T12: -0.0245 REMARK 3 T13: 0.0654 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.0023 L22: 0.0038 REMARK 3 L33: 0.0041 L12: -0.0016 REMARK 3 L13: -0.0060 L23: 0.0056 REMARK 3 S TENSOR REMARK 3 S11: -0.0520 S12: 0.0876 S13: -0.1524 REMARK 3 S21: -0.0279 S22: 0.1458 S23: 0.2576 REMARK 3 S31: 0.1923 S32: -0.1455 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 90 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9294 52.7871 51.2608 REMARK 3 T TENSOR REMARK 3 T11: 0.2167 T22: 0.1935 REMARK 3 T33: 0.2038 T12: -0.0269 REMARK 3 T13: 0.0669 T23: -0.0374 REMARK 3 L TENSOR REMARK 3 L11: 0.0796 L22: 0.0339 REMARK 3 L33: 0.0095 L12: 0.0199 REMARK 3 L13: 0.0226 L23: 0.0158 REMARK 3 S TENSOR REMARK 3 S11: -0.0643 S12: 0.1362 S13: 0.0932 REMARK 3 S21: -0.1607 S22: 0.0920 S23: 0.0342 REMARK 3 S31: 0.0252 S32: -0.0486 S33: 0.0109 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0633 66.4028 68.3360 REMARK 3 T TENSOR REMARK 3 T11: 0.1994 T22: 0.1858 REMARK 3 T33: 0.2511 T12: 0.0060 REMARK 3 T13: 0.0267 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.0232 L22: 0.0131 REMARK 3 L33: 0.0060 L12: -0.0167 REMARK 3 L13: -0.0041 L23: 0.0081 REMARK 3 S TENSOR REMARK 3 S11: 0.0224 S12: -0.0435 S13: 0.0165 REMARK 3 S21: 0.0674 S22: -0.0137 S23: -0.1976 REMARK 3 S31: 0.0195 S32: 0.0844 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0191 63.7788 70.8345 REMARK 3 T TENSOR REMARK 3 T11: 0.2195 T22: 0.1884 REMARK 3 T33: 0.2101 T12: 0.0461 REMARK 3 T13: -0.0100 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 0.0013 L22: 0.0121 REMARK 3 L33: 0.0088 L12: 0.0050 REMARK 3 L13: 0.0034 L23: 0.0114 REMARK 3 S TENSOR REMARK 3 S11: -0.0183 S12: -0.0687 S13: 0.0962 REMARK 3 S21: 0.0082 S22: 0.0291 S23: 0.0266 REMARK 3 S31: -0.0121 S32: 0.0811 S33: -0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 141 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6886 53.9595 80.8644 REMARK 3 T TENSOR REMARK 3 T11: 0.2894 T22: 0.2573 REMARK 3 T33: 0.2413 T12: 0.0788 REMARK 3 T13: -0.0328 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 0.0041 L22: 0.0139 REMARK 3 L33: 0.0127 L12: 0.0080 REMARK 3 L13: 0.0000 L23: -0.0035 REMARK 3 S TENSOR REMARK 3 S11: -0.1241 S12: -0.1299 S13: -0.0877 REMARK 3 S21: 0.1703 S22: 0.1207 S23: -0.1060 REMARK 3 S31: -0.1701 S32: 0.0323 S33: -0.0001 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0452 51.0924 82.1809 REMARK 3 T TENSOR REMARK 3 T11: 0.2135 T22: 0.3785 REMARK 3 T33: 0.2053 T12: 0.1211 REMARK 3 T13: 0.0446 T23: 0.0781 REMARK 3 L TENSOR REMARK 3 L11: 0.0097 L22: 0.0394 REMARK 3 L33: 0.0244 L12: 0.0173 REMARK 3 L13: -0.0076 L23: 0.0092 REMARK 3 S TENSOR REMARK 3 S11: -0.0595 S12: -0.2010 S13: -0.0127 REMARK 3 S21: -0.0348 S22: 0.2270 S23: 0.0650 REMARK 3 S31: -0.1748 S32: -0.1972 S33: 0.0740 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 183 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9092 41.0226 86.6089 REMARK 3 T TENSOR REMARK 3 T11: 0.2211 T22: 0.4476 REMARK 3 T33: 0.2572 T12: -0.0187 REMARK 3 T13: -0.0162 T23: 0.1985 REMARK 3 L TENSOR REMARK 3 L11: 0.2180 L22: 0.3443 REMARK 3 L33: 0.2268 L12: 0.2634 REMARK 3 L13: 0.2071 L23: 0.2713 REMARK 3 S TENSOR REMARK 3 S11: 0.0646 S12: -0.1006 S13: -0.2325 REMARK 3 S21: -0.0174 S22: 0.3957 S23: 0.0566 REMARK 3 S31: -0.0093 S32: -0.2805 S33: 0.2933 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 206 THROUGH 232 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.3859 39.5992 74.9934 REMARK 3 T TENSOR REMARK 3 T11: 0.2653 T22: 0.1743 REMARK 3 T33: 0.2211 T12: 0.0523 REMARK 3 T13: -0.0562 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 0.8060 L22: 0.0437 REMARK 3 L33: 0.1279 L12: 0.1136 REMARK 3 L13: -0.1786 L23: -0.0150 REMARK 3 S TENSOR REMARK 3 S11: 0.1646 S12: -0.2518 S13: -0.0559 REMARK 3 S21: -0.0928 S22: 0.0396 S23: 0.0119 REMARK 3 S31: 0.0978 S32: 0.0707 S33: 0.0590 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 233 THROUGH 259 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.5917 30.1941 77.5327 REMARK 3 T TENSOR REMARK 3 T11: 0.3028 T22: 0.5139 REMARK 3 T33: 0.3873 T12: -0.2549 REMARK 3 T13: -0.3864 T23: 0.2426 REMARK 3 L TENSOR REMARK 3 L11: 0.1110 L22: 0.1859 REMARK 3 L33: 0.2179 L12: -0.1223 REMARK 3 L13: 0.0983 L23: -0.1154 REMARK 3 S TENSOR REMARK 3 S11: 0.2920 S12: -0.2159 S13: -0.2658 REMARK 3 S21: -0.0975 S22: 0.2614 S23: 0.1161 REMARK 3 S31: 0.3586 S32: -0.3519 S33: 0.8198 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 260 THROUGH 274 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.9576 39.6971 83.5844 REMARK 3 T TENSOR REMARK 3 T11: 0.1792 T22: 0.6971 REMARK 3 T33: 0.4375 T12: -0.0504 REMARK 3 T13: -0.1685 T23: 0.4088 REMARK 3 L TENSOR REMARK 3 L11: 0.0065 L22: 0.0040 REMARK 3 L33: 0.0183 L12: -0.0036 REMARK 3 L13: 0.0070 L23: -0.0067 REMARK 3 S TENSOR REMARK 3 S11: 0.0635 S12: -0.0172 S13: 0.0553 REMARK 3 S21: 0.0389 S22: -0.0209 S23: 0.0752 REMARK 3 S31: 0.0502 S32: -0.1685 S33: -0.0160 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 4MB7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081695. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91730 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 64.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 0.66500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SOLVE 2.15, RESOLVE 2.15 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) POLYETHYLENE GLYCOL 3350, REMARK 280 AND 0.2 M SODIUM SULFATE DECAHYDRATE , PH 6.8, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 60.83500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.12310 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 54.72667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 60.83500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 35.12310 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 54.72667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 60.83500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 35.12310 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 54.72667 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 60.83500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 35.12310 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 54.72667 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 60.83500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 35.12310 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 54.72667 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 60.83500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 35.12310 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 54.72667 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 70.24621 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 109.45333 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 70.24621 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 109.45333 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 70.24621 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 109.45333 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 70.24621 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 109.45333 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 70.24621 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 109.45333 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 70.24621 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 109.45333 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -104.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 164.18000 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 509 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 510 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 519 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 534 LIES ON A SPECIAL POSITION. 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 31 CD CE NZ REMARK 470 LYS A 44 CD CE NZ REMARK 470 GLN A 81 CD OE1 NE2 REMARK 470 ASP A 82 CG OD1 OD2 REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 ARG A 87 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 104 CD NE CZ NH1 NH2 REMARK 470 LYS A 136 CD CE NZ REMARK 470 ARG A 146 NE CZ NH1 NH2 REMARK 470 ASN A 161 CG OD1 ND2 REMARK 470 SER A 165 OG REMARK 470 LYS A 200 CE NZ REMARK 470 GLU A 206 CG CD OE1 OE2 REMARK 470 LYS A 228 CE NZ REMARK 470 LYS A 253 CD CE NZ REMARK 470 ARG A 256 NE CZ NH1 NH2 REMARK 470 LYS A 257 CD CE NZ REMARK 470 LYS A 258 CD CE NZ REMARK 470 LEU A 261 CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O MET A 265 O HOH A 500 2.16 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 ARG A 87 2.12 81.47 REMARK 500 TYR A 122 -17.49 -140.90 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 248 SG REMARK 620 2 HIS A 252 ND1 103.7 REMARK 620 3 CYS A 269 SG 127.6 101.2 REMARK 620 4 CYS A 272 SG 117.1 96.7 104.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 304 DBREF 4MB7 A 2 274 UNP Q5UNW7 YL720_MIMIV 2 274 SEQRES 1 A 273 VAL GLU ALA PRO ARG ILE ARG ILE THR TYR GLU LYS ILE SEQRES 2 A 273 ARG HIS THR LYS ASN HIS ARG ILE VAL SER ILE SER GLY SEQRES 3 A 273 PRO SER TYR LYS ARG MET ASN VAL ASP LEU ILE ASP TYR SEQRES 4 A 273 ILE ILE ARG LYS TRP TRP PHE ALA GLY LYS TYR ILE TYR SEQRES 5 A 273 LEU MET LEU ILE SER SER ASN LYS PRO THR TYR VAL ILE SEQRES 6 A 273 ARG THR HIS MET MET MET HIS GLY ARG ILE LEU VAL GLY SEQRES 7 A 273 ASN GLN ASP SER PRO THR LYS ARG ALA PHE MET ILE ILE SEQRES 8 A 273 GLN LEU ASP ASN ASP ILE VAL LEU ARG TRP TYR ARG SER SEQRES 9 A 273 GLN ILE THR LEU LEU ASP PRO ASN CYS LEU ALA GLU ILE SEQRES 10 A 273 LYS THR ASN TYR THR ILE CYS THR THR ARG GLN ALA ILE SEQRES 11 A 273 MET ASP SER ILE LYS LEU MET LYS TYR ASP LEU SER ASN SEQRES 12 A 273 ASN ARG PHE ASP TYR ASN LEU PHE GLN SER HIS LEU LYS SEQRES 13 A 273 ASN GLY ILE ASN ILE HIS SER SER GLU ILE ILE THR ASP SEQRES 14 A 273 PHE LEU LEU ASP GLN GLU TYR PHE PRO GLY VAL GLY ASN SEQRES 15 A 273 ILE LEU GLN GLN GLU ALA LEU TYR ASP CYS LYS ILE LEU SEQRES 16 A 273 PRO LEU LYS LYS VAL GLN ASP ILE ASP GLU PRO MET PHE SEQRES 17 A 273 ASP CYS LEU CYS ASN SER LEU LYS LYS ILE ILE ASP LEU SEQRES 18 A 273 LEU TYR GLU SER TYR LYS PHE ARG GLU SER GLY LYS GLU SEQRES 19 A 273 PHE GLY PRO ILE LEU ARG ILE TYR ARG LYS SER LEU CYS SEQRES 20 A 273 PRO LEU GLY HIS LYS THR ILE ARG LYS LYS ILE GLY LEU SEQRES 21 A 273 ARG ASN ARG MET THR THR TRP CYS PRO VAL CYS GLN LEU HET ZN A 301 1 HET SO4 A 302 5 HET SO4 A 303 5 HET SO4 A 304 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *182(H2 O) HELIX 1 1 PRO A 5 ARG A 15 1 11 HELIX 2 2 HIS A 16 LYS A 18 5 3 HELIX 3 3 GLY A 27 ASN A 34 1 8 HELIX 4 4 THR A 127 MET A 138 1 12 HELIX 5 5 LYS A 139 ASP A 141 5 3 HELIX 6 6 ASP A 148 HIS A 163 1 16 HELIX 7 7 ILE A 167 LEU A 173 1 7 HELIX 8 8 GLY A 182 CYS A 193 1 12 HELIX 9 9 LYS A 200 ILE A 204 5 5 HELIX 10 10 ASP A 205 SER A 232 1 28 SHEET 1 A 6 ILE A 22 SER A 26 0 SHEET 2 A 6 MET A 90 LEU A 94 -1 O ILE A 91 N SER A 26 SHEET 3 A 6 VAL A 99 LEU A 110 -1 O LEU A 100 N ILE A 92 SHEET 4 A 6 TYR A 64 GLY A 79 -1 N VAL A 65 O LEU A 110 SHEET 5 A 6 TYR A 51 ILE A 57 -1 N LEU A 56 O TYR A 64 SHEET 6 A 6 ILE A 41 ALA A 48 -1 N TRP A 46 O TYR A 53 SHEET 1 B 2 GLU A 117 LYS A 119 0 SHEET 2 B 2 ILE A 124 THR A 126 -1 O CYS A 125 N ILE A 118 SHEET 1 C 2 ILE A 255 ILE A 259 0 SHEET 2 C 2 ARG A 264 TRP A 268 -1 O THR A 266 N LYS A 257 LINK SG CYS A 248 ZN ZN A 301 1555 1555 2.24 LINK ND1 HIS A 252 ZN ZN A 301 1555 1555 2.03 LINK SG CYS A 269 ZN ZN A 301 1555 1555 2.26 LINK SG CYS A 272 ZN ZN A 301 1555 1555 2.34 CISPEP 1 ALA A 4 PRO A 5 0 0.63 SITE 1 AC1 4 CYS A 248 HIS A 252 CYS A 269 CYS A 272 SITE 1 AC2 5 ARG A 6 LYS A 13 TYR A 227 ARG A 230 SITE 2 AC2 5 GLU A 231 SITE 1 AC3 6 VAL A 2 LYS A 50 GLY A 182 ASN A 183 SITE 2 AC3 6 ARG A 264 HOH A 574 SITE 1 AC4 6 LYS A 50 HIS A 69 ASN A 121 GLN A 175 SITE 2 AC4 6 HOH A 573 HOH A 576 CRYST1 121.670 121.670 164.180 90.00 90.00 120.00 H 3 2 18 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 0.008219 0.004745 0.000000 0.00000 SCALE2 0.000000 0.009490 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006091 0.00000