HEADER HYDROLASE 01-JUL-21 7RAG TITLE STRUCTURE OF THE CWLD AMIDASE FROM CLOSTRIDIOIDES DIFFICILE IN COMPLEX TITLE 2 WITH THE GERS LIPOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LIPOPROTEIN LOCALISATION LOLA/LOLB/LPPX,OUTER MEMBRANE COMPND 5 LIPOPROTEIN-SORTING PROTEIN,PUTATIVE LIPOPROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GERMINATION-SPECIFIC N-ACETYLMURAMOYL-L-ALANINE AMIDASE, COMPND 9 AUTOLYSIN; COMPND 10 CHAIN: B; COMPND 11 EC: 3.5.1.28; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIOIDES DIFFICILE; SOURCE 3 ORGANISM_COMMON: PEPTOCLOSTRIDIUM DIFFICILE; SOURCE 4 ORGANISM_TAXID: 1496; SOURCE 5 GENE: BN1096_760049, BN1097_760051, CDGR_15010, E5F32_07620, SOURCE 6 E5F39_08860, E5F43_07640, GSQ22_27115, IB136_2570, SOURCE 7 SAMEA1402406_02874, SAMEA3374989_03440, SAMEA3375041_03139, SOURCE 8 SAMEA708418_02871; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: CLOSTRIDIOIDES DIFFICILE; SOURCE 13 ORGANISM_COMMON: PEPTOCLOSTRIDIUM DIFFICILE; SOURCE 14 ORGANISM_TAXID: 1496; SOURCE 15 GENE: CWLD, CD630_01060; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS N-ACETYLMURAMIC ACID (NAM) HYDROLASE CORTEX LYTIC ENZYME AMIDASE_3 KEYWDS 2 FAMILY LOLA FAMILY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.E.ECKENROTH,S.DOUBLIE REVDAT 2 06-OCT-21 7RAG 1 JRNL REVDAT 1 08-SEP-21 7RAG 0 JRNL AUTH C.ALVES FELICIANO,B.E.ECKENROTH,O.R.DIAZ,S.DOUBLIE,A.SHEN JRNL TITL A LIPOPROTEIN ALLOSTERICALLY ACTIVATES THE CWLD AMIDASE JRNL TITL 2 DURING CLOSTRIDIOIDES DIFFICILE SPORE FORMATION. JRNL REF PLOS GENET. V. 17 09791 2021 JRNL REFN ESSN 1553-7404 JRNL PMID 34570752 JRNL DOI 10.1371/JOURNAL.PGEN.1009791 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 37340 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3742 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 45.5500 - 7.2000 0.99 1252 129 0.1756 0.1990 REMARK 3 2 7.1900 - 5.7200 1.00 1250 143 0.1947 0.2183 REMARK 3 3 5.7100 - 4.9900 1.00 1211 176 0.1880 0.2023 REMARK 3 4 4.9900 - 4.5400 1.00 1254 134 0.1521 0.2123 REMARK 3 5 4.5400 - 4.2100 1.00 1244 132 0.1457 0.1895 REMARK 3 6 4.2100 - 3.9600 1.00 1287 112 0.1612 0.2081 REMARK 3 7 3.9600 - 3.7600 1.00 1262 123 0.1756 0.2091 REMARK 3 8 3.7600 - 3.6000 1.00 1286 103 0.2056 0.2499 REMARK 3 9 3.6000 - 3.4600 1.00 1238 150 0.1964 0.3164 REMARK 3 10 3.4600 - 3.3400 1.00 1232 157 0.2045 0.2804 REMARK 3 11 3.3400 - 3.2400 1.00 1241 141 0.2168 0.2689 REMARK 3 12 3.2400 - 3.1500 1.00 1250 128 0.2255 0.2165 REMARK 3 13 3.1400 - 3.0600 1.00 1245 136 0.2394 0.3167 REMARK 3 14 3.0600 - 2.9900 1.00 1262 116 0.2452 0.3191 REMARK 3 15 2.9900 - 2.9200 1.00 1239 139 0.2376 0.3160 REMARK 3 16 2.9200 - 2.8600 1.00 1278 150 0.2574 0.3233 REMARK 3 17 2.8600 - 2.8000 1.00 1235 143 0.2432 0.3435 REMARK 3 18 2.8000 - 2.7500 1.00 1209 144 0.2675 0.2839 REMARK 3 19 2.7500 - 2.7000 1.00 1231 155 0.2847 0.3135 REMARK 3 20 2.7000 - 2.6500 1.00 1252 149 0.2871 0.3535 REMARK 3 21 2.6500 - 2.6100 1.00 1247 144 0.2969 0.3604 REMARK 3 22 2.6100 - 2.5700 1.00 1222 138 0.3146 0.3309 REMARK 3 23 2.5700 - 2.5300 1.00 1257 138 0.3105 0.3989 REMARK 3 24 2.5300 - 2.5000 1.00 1229 140 0.3461 0.3828 REMARK 3 25 2.5000 - 2.4600 1.00 1235 148 0.3509 0.3576 REMARK 3 26 2.4600 - 2.4300 1.00 1243 154 0.3654 0.4148 REMARK 3 27 2.4300 - 2.4000 0.96 1207 120 0.3826 0.3871 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) : 30.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.18 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 : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 22 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.5868 41.4828 65.7657 REMARK 3 T TENSOR REMARK 3 T11: 0.6323 T22: 0.8998 REMARK 3 T33: 0.6767 T12: 0.0621 REMARK 3 T13: 0.0446 T23: -0.0211 REMARK 3 L TENSOR REMARK 3 L11: -0.2245 L22: 1.5458 REMARK 3 L33: -0.3096 L12: -0.3838 REMARK 3 L13: -0.5983 L23: -0.8006 REMARK 3 S TENSOR REMARK 3 S11: 0.0601 S12: 0.0666 S13: -0.2832 REMARK 3 S21: -0.3272 S22: -0.0952 S23: 0.3850 REMARK 3 S31: 0.3138 S32: -0.1989 S33: 0.0023 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.1770 53.7241 34.4524 REMARK 3 T TENSOR REMARK 3 T11: 0.7374 T22: 0.6388 REMARK 3 T33: 0.5634 T12: 0.1788 REMARK 3 T13: 0.0376 T23: -0.0619 REMARK 3 L TENSOR REMARK 3 L11: 0.9215 L22: 5.4130 REMARK 3 L33: 0.9669 L12: 1.1292 REMARK 3 L13: -0.2549 L23: -0.1991 REMARK 3 S TENSOR REMARK 3 S11: -0.0827 S12: -0.0893 S13: -0.2509 REMARK 3 S21: 0.5097 S22: 0.1781 S23: 0.3425 REMARK 3 S31: 0.2350 S32: -0.0643 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 40 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.1547 81.0789 19.4406 REMARK 3 T TENSOR REMARK 3 T11: 0.8587 T22: 0.6552 REMARK 3 T33: 0.6585 T12: 0.0032 REMARK 3 T13: 0.1815 T23: -0.0678 REMARK 3 L TENSOR REMARK 3 L11: 1.3904 L22: 1.6269 REMARK 3 L33: 1.9292 L12: -0.1513 REMARK 3 L13: 1.4061 L23: 0.7913 REMARK 3 S TENSOR REMARK 3 S11: 0.0950 S12: 0.3255 S13: 0.6381 REMARK 3 S21: -0.8223 S22: 0.2966 S23: -0.1475 REMARK 3 S31: -0.4557 S32: 0.3965 S33: -0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 65 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.3620 71.8534 23.8547 REMARK 3 T TENSOR REMARK 3 T11: 0.5753 T22: 0.6005 REMARK 3 T33: 0.5716 T12: 0.1311 REMARK 3 T13: 0.0997 T23: -0.1126 REMARK 3 L TENSOR REMARK 3 L11: 1.8277 L22: 0.9568 REMARK 3 L33: 1.2032 L12: -0.3523 REMARK 3 L13: 0.7347 L23: 0.7660 REMARK 3 S TENSOR REMARK 3 S11: -0.1039 S12: -0.1157 S13: -0.0080 REMARK 3 S21: -1.2805 S22: -0.0958 S23: -1.1286 REMARK 3 S31: 0.7371 S32: 0.4876 S33: -0.0004 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 84 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0817 77.6726 13.8086 REMARK 3 T TENSOR REMARK 3 T11: 0.8963 T22: 0.9057 REMARK 3 T33: 0.5027 T12: -0.0462 REMARK 3 T13: -0.0626 T23: 0.0651 REMARK 3 L TENSOR REMARK 3 L11: 1.8959 L22: 1.1969 REMARK 3 L33: 0.8821 L12: 0.0495 REMARK 3 L13: -0.5786 L23: 0.9070 REMARK 3 S TENSOR REMARK 3 S11: -0.4404 S12: 1.2459 S13: 0.1196 REMARK 3 S21: -1.7094 S22: 0.3281 S23: -0.2072 REMARK 3 S31: 1.0631 S32: -0.4347 S33: -0.0005 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 106 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.3198 82.0185 21.6102 REMARK 3 T TENSOR REMARK 3 T11: 0.6198 T22: 0.7166 REMARK 3 T33: 0.6726 T12: 0.1512 REMARK 3 T13: 0.0069 T23: 0.0433 REMARK 3 L TENSOR REMARK 3 L11: 1.7956 L22: 2.0399 REMARK 3 L33: 0.8828 L12: -0.1598 REMARK 3 L13: -0.5333 L23: 1.1616 REMARK 3 S TENSOR REMARK 3 S11: 0.0103 S12: 0.3930 S13: 0.2711 REMARK 3 S21: -0.0541 S22: 0.2716 S23: 0.4193 REMARK 3 S31: -0.3423 S32: -0.2726 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 134 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.2689 91.2878 26.9276 REMARK 3 T TENSOR REMARK 3 T11: 0.7771 T22: 0.7259 REMARK 3 T33: 1.2543 T12: -0.0901 REMARK 3 T13: 0.1066 T23: -0.2284 REMARK 3 L TENSOR REMARK 3 L11: 0.0876 L22: 0.1043 REMARK 3 L33: 0.0667 L12: 0.1248 REMARK 3 L13: -0.0896 L23: -0.1010 REMARK 3 S TENSOR REMARK 3 S11: 0.2909 S12: -0.6113 S13: 1.2880 REMARK 3 S21: 0.1405 S22: 0.0284 S23: -1.5215 REMARK 3 S31: -0.2737 S32: 0.3824 S33: -0.0022 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 146 THROUGH 171 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1409 83.1827 38.4617 REMARK 3 T TENSOR REMARK 3 T11: 0.6666 T22: 0.6198 REMARK 3 T33: 0.6641 T12: 0.1115 REMARK 3 T13: -0.0660 T23: -0.1994 REMARK 3 L TENSOR REMARK 3 L11: 0.8794 L22: 2.0168 REMARK 3 L33: 1.0395 L12: 1.2622 REMARK 3 L13: 0.4745 L23: 0.4538 REMARK 3 S TENSOR REMARK 3 S11: -0.0487 S12: -0.7337 S13: 0.5411 REMARK 3 S21: 0.9969 S22: 0.1775 S23: -0.2184 REMARK 3 S31: 0.0763 S32: 0.1424 S33: -0.0004 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 172 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.2154 85.6351 38.6096 REMARK 3 T TENSOR REMARK 3 T11: 0.7116 T22: 0.8057 REMARK 3 T33: 1.0395 T12: 0.0120 REMARK 3 T13: -0.0863 T23: -0.3895 REMARK 3 L TENSOR REMARK 3 L11: 0.0473 L22: -0.0107 REMARK 3 L33: 0.1207 L12: -0.0132 REMARK 3 L13: -0.0630 L23: 0.0029 REMARK 3 S TENSOR REMARK 3 S11: -0.0866 S12: -0.9957 S13: -0.1949 REMARK 3 S21: 0.8250 S22: 0.3601 S23: -1.0098 REMARK 3 S31: -0.7685 S32: 0.1504 S33: -0.0027 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 180 THROUGH 193 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.2508 88.6112 30.1042 REMARK 3 T TENSOR REMARK 3 T11: 0.8004 T22: 0.5690 REMARK 3 T33: 0.8868 T12: 0.1987 REMARK 3 T13: 0.0224 T23: -0.0476 REMARK 3 L TENSOR REMARK 3 L11: 0.5588 L22: 0.7671 REMARK 3 L33: 0.4777 L12: -0.6117 REMARK 3 L13: 0.2277 L23: 0.1602 REMARK 3 S TENSOR REMARK 3 S11: -0.3798 S12: -0.5922 S13: 1.3849 REMARK 3 S21: 0.6985 S22: 0.3817 S23: 0.4532 REMARK 3 S31: -1.0237 S32: -0.6252 S33: -0.0017 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 194 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.7107 83.0724 26.1822 REMARK 3 T TENSOR REMARK 3 T11: 0.6254 T22: 0.7077 REMARK 3 T33: 1.0830 T12: -0.0120 REMARK 3 T13: 0.2766 T23: -0.1585 REMARK 3 L TENSOR REMARK 3 L11: 0.0957 L22: 0.2654 REMARK 3 L33: 0.5655 L12: -0.0957 REMARK 3 L13: 0.0542 L23: 0.1894 REMARK 3 S TENSOR REMARK 3 S11: 0.1692 S12: -0.1765 S13: 0.5391 REMARK 3 S21: -0.5592 S22: 0.0770 S23: -0.9604 REMARK 3 S31: -0.3759 S32: 0.3964 S33: -0.0001 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 215 THROUGH 236 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.2265 72.3706 34.6577 REMARK 3 T TENSOR REMARK 3 T11: 0.5457 T22: 0.5461 REMARK 3 T33: 0.5993 T12: 0.1655 REMARK 3 T13: -0.0400 T23: -0.1399 REMARK 3 L TENSOR REMARK 3 L11: 1.3332 L22: 2.9465 REMARK 3 L33: 1.2582 L12: 0.2793 REMARK 3 L13: 1.1495 L23: -0.5585 REMARK 3 S TENSOR REMARK 3 S11: 0.0054 S12: -0.0820 S13: 0.3938 REMARK 3 S21: 0.6062 S22: 0.1689 S23: -0.8458 REMARK 3 S31: -0.0911 S32: 0.0154 S33: 0.0004 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 7RAG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000257900. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-20 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 : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS V3 REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS V3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37392 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 45.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.04800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 24.90 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP 2.8.10 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12-18 % PEG 3350, 5 % GLYCEROL, 0.25 M REMARK 280 AMMONIUM NITRATE, 50 MM BISTRIS PH 7.5. 1:1 RATIO OF RESERVOIR REMARK 280 TO 30 MG/ML COMPLEX, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 103.18067 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 51.59033 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 77.38550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.79517 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 128.97583 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 103.18067 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 51.59033 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.79517 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 77.38550 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 128.97583 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: 13800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 103.18067 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 LYS A 115 REMARK 465 ASN A 116 REMARK 465 ASN A 117 REMARK 465 GLN A 118 REMARK 465 ASN A 196 REMARK 465 MSE B 25 REMARK 465 LYS B 26 REMARK 465 ASN B 27 REMARK 465 ILE B 28 REMARK 465 SER B 29 REMARK 465 GLU B 30 REMARK 465 ASP B 31 REMARK 465 VAL B 32 REMARK 465 ILE B 33 REMARK 465 LYS B 34 REMARK 465 TYR B 35 REMARK 465 MSE B 36 REMARK 465 PRO B 37 REMARK 465 VAL B 38 REMARK 465 THR B 39 REMARK 465 LYS B 237 REMARK 465 LEU B 238 REMARK 465 ALA B 239 REMARK 465 ALA B 240 REMARK 465 ALA B 241 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 34 CE NZ REMARK 470 LYS A 70 CD CE NZ REMARK 470 ASP A 95 CG OD1 OD2 REMARK 470 LYS A 96 CG CD CE NZ REMARK 470 TYR A 119 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 132 CG OD1 ND2 REMARK 470 GLU A 133 CG CD OE1 OE2 REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 LYS A 136 CD CE NZ REMARK 470 LYS A 141 CG CD CE NZ REMARK 470 ASP A 153 CG OD1 OD2 REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 LYS B 59 CG CD CE NZ REMARK 470 LYS B 99 CG CD CE NZ REMARK 470 GLU B 101 CG CD OE1 OE2 REMARK 470 ASN B 103 CG OD1 ND2 REMARK 470 LYS B 104 CG CD CE NZ REMARK 470 GLN B 108 CG CD OE1 NE2 REMARK 470 LYS B 109 CG CD CE NZ REMARK 470 LYS B 115 CG CD CE NZ REMARK 470 GLU B 119 CG CD OE1 OE2 REMARK 470 GLU B 138 CG CD OE1 OE2 REMARK 470 GLN B 139 CG CD OE1 NE2 REMARK 470 LYS B 141 CG CD CE NZ REMARK 470 GLU B 206 CG CD OE1 OE2 REMARK 470 LYS B 207 CG CD CE NZ REMARK 470 LYS B 210 CG CD CE NZ REMARK 470 ASP B 236 CG OD1 OD2 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 LYS A 58 -149.08 -147.54 REMARK 500 ASP A 95 2.32 -64.97 REMARK 500 LYS A 127 -5.90 78.60 REMARK 500 GLU A 133 -156.64 -137.96 REMARK 500 LYS A 169 18.04 56.07 REMARK 500 HIS B 49 -163.95 148.04 REMARK 500 PRO B 54 -178.09 -69.28 REMARK 500 GLU B 100 94.77 -69.69 REMARK 500 ASP B 172 103.83 -161.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY B 48 HIS B 49 138.94 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 B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MSE A 22 N REMARK 620 2 MSE A 22 O 87.1 REMARK 620 3 HIS B 49 NE2 154.8 69.4 REMARK 620 4 GLU B 65 OE1 152.9 67.5 2.0 REMARK 620 5 HIS B 133 ND1 154.2 69.3 1.3 2.1 REMARK 620 N 1 2 3 4 DBREF1 7RAG A 23 196 UNP A0A031WJD5_CLODI DBREF2 7RAG A A0A031WJD5 23 196 DBREF 7RAG B 26 234 UNP Q18CJ4 Q18CJ4_CLOD6 26 234 SEQADV 7RAG MSE A 22 UNP A0A031WJD INITIATING METHIONINE SEQADV 7RAG MSE B 25 UNP Q18CJ4 INITIATING METHIONINE SEQADV 7RAG VAL B 235 UNP Q18CJ4 EXPRESSION TAG SEQADV 7RAG ASP B 236 UNP Q18CJ4 EXPRESSION TAG SEQADV 7RAG LYS B 237 UNP Q18CJ4 EXPRESSION TAG SEQADV 7RAG LEU B 238 UNP Q18CJ4 EXPRESSION TAG SEQADV 7RAG ALA B 239 UNP Q18CJ4 EXPRESSION TAG SEQADV 7RAG ALA B 240 UNP Q18CJ4 EXPRESSION TAG SEQADV 7RAG ALA B 241 UNP Q18CJ4 EXPRESSION TAG SEQRES 1 A 175 MSE GLN LYS ARG GLN SER THR LYS GLU GLU VAL TYR LYS SEQRES 2 A 175 ASP PHE GLN LYS GLN ILE SER ASP MSE ASN TYR TYR SER SEQRES 3 A 175 CYS LYS ALA GLU VAL GLU VAL VAL GLY ASN LYS SER PRO SEQRES 4 A 175 HIS ASN TYR VAL LEU ILE HIS THR TYR LYS LYS THR ASP SEQRES 5 A 175 ASN TYR LYS LEU GLU VAL ILE SER PRO LYS HIS LEU LYS SEQRES 6 A 175 GLY LYS SER ILE GLU TYR GLN GLY ASP LYS ILE LEU VAL SEQRES 7 A 175 LYS ASN PRO LYS ILE SER ASP VAL VAL GLU LEU PRO ASN SEQRES 8 A 175 THR GLY LYS ASN ASN GLN TYR LEU PHE VAL GLY ASP PHE SEQRES 9 A 175 ILE LYS ASN TYR LEU GLN ASN GLU GLU MSE LYS VAL LYS SEQRES 10 A 175 LEU SER LYS GLY HIS LEU VAL LEU GLU THR PHE ILE PRO SEQRES 11 A 175 GLY ASP ASN LYS TYR PHE ASN LYS GLN VAL LEU TYR VAL SEQRES 12 A 175 ASN ALA ASP THR LYS ASN PRO GLU LYS MSE GLU VAL LEU SEQRES 13 A 175 ASP LYS GLU GLY VAL PRO ARG PHE THR VAL LYS TYR LYS SEQRES 14 A 175 ASP PHE GLU TYR ARG ASN SEQRES 1 B 217 MSE LYS ASN ILE SER GLU ASP VAL ILE LYS TYR MSE PRO SEQRES 2 B 217 VAL THR ASN LYS THR ILE ILE LEU ASP ALA GLY HIS GLY SEQRES 3 B 217 GLY ILE ASP PRO GLY ALA LEU ASN LYS ASP LYS SER THR SEQRES 4 B 217 SER GLU LYS ASP ILE ASN LEU ALA ILE THR LEU LYS LEU SEQRES 5 B 217 ARG GLU LEU ILE GLU SER SER GLY GLY LEU VAL ILE LEU SEQRES 6 B 217 THR ARG GLU ASP ASP SER SER LEU TYR LYS GLU GLU ASN SEQRES 7 B 217 ASN LYS THR THR ARG GLN LYS TYR ASN GLU ASN LEU LYS SEQRES 8 B 217 ASN ARG LYS GLU ILE ILE SER ASN SER ASN ALA ASN MSE SEQRES 9 B 217 PHE VAL SER ILE HIS LEU ASN ALA PHE GLU GLN SER LYS SEQRES 10 B 217 TYR TYR GLY ALA GLN THR PHE TYR PRO LYS ASP LYS GLN SEQRES 11 B 217 ASP SER LYS GLU LEU SER LYS CYS ILE GLN GLU GLU LEU SEQRES 12 B 217 LYS ARG VAL VAL ASP LYS THR ASN ASN ARG GLU VAL LYS SEQRES 13 B 217 PRO ARG ASP ASP ILE TYR LEU LEU LYS ASP ASN ASN ILE SEQRES 14 B 217 PRO SER VAL LEU ILE GLU CYS GLY PHE LEU SER ASN GLU SEQRES 15 B 217 LYS GLU CYS LYS LEU LEU THR ASP GLU THR TYR GLN GLU SEQRES 16 B 217 LYS ILE ALA TRP ALA ILE TYR ILE GLY ILE GLN LYS TYR SEQRES 17 B 217 LEU SER VAL ASP LYS LEU ALA ALA ALA MODRES 7RAG MSE A 43 MET MODIFIED RESIDUE MODRES 7RAG MSE A 135 MET MODIFIED RESIDUE MODRES 7RAG MSE A 174 MET MODIFIED RESIDUE MODRES 7RAG MSE B 128 MET MODIFIED RESIDUE HET MSE A 22 8 HET MSE A 43 8 HET MSE A 135 8 HET MSE A 174 8 HET MSE B 128 8 HET ZN B 301 1 HET EDO B 302 4 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 3 ZN ZN 2+ FORMUL 4 EDO C2 H6 O2 FORMUL 5 HOH *14(H2 O) HELIX 1 AA1 THR A 28 MSE A 43 1 16 HELIX 2 AA2 PRO A 82 LYS A 86 5 5 HELIX 3 AA3 PRO A 102 SER A 105 5 4 HELIX 4 AA4 SER B 64 SER B 83 1 20 HELIX 5 AA5 THR B 105 SER B 124 1 20 HELIX 6 AA6 LYS B 153 ASP B 172 1 20 HELIX 7 AA7 ILE B 185 LYS B 189 5 5 HELIX 8 AA8 ASN B 205 THR B 213 1 9 HELIX 9 AA9 ASP B 214 ASP B 236 1 23 SHEET 1 AA1 2 TYR A 45 VAL A 54 0 SHEET 2 AA1 2 HIS A 61 LYS A 70 -1 O LEU A 65 N ALA A 50 SHEET 1 AA2 4 TYR A 75 GLU A 78 0 SHEET 2 AA2 4 SER A 89 TYR A 92 -1 O TYR A 92 N TYR A 75 SHEET 3 AA2 4 LYS A 96 ASN A 101 -1 O LYS A 100 N SER A 89 SHEET 4 AA2 4 ASP A 106 PRO A 111 -1 O VAL A 108 N VAL A 99 SHEET 1 AA3 5 LYS A 136 SER A 140 0 SHEET 2 AA3 5 HIS A 143 PHE A 149 -1 O VAL A 145 N LYS A 138 SHEET 3 AA3 5 LYS A 159 ASN A 165 -1 O GLN A 160 N THR A 148 SHEET 4 AA3 5 PRO A 171 LEU A 177 -1 O LYS A 173 N TYR A 163 SHEET 5 AA3 5 PRO A 183 LYS A 188 -1 O ARG A 184 N VAL A 176 SHEET 1 AA4 6 LEU B 86 LEU B 89 0 SHEET 2 AA4 6 THR B 42 ALA B 47 1 N ILE B 43 O ILE B 88 SHEET 3 AA4 6 MSE B 128 ASN B 135 1 O VAL B 130 N ILE B 44 SHEET 4 AA4 6 SER B 195 PHE B 202 1 O ILE B 198 N HIS B 133 SHEET 5 AA4 6 GLN B 146 PRO B 150 -1 N GLN B 146 O GLU B 199 SHEET 6 AA4 6 LYS B 180 ARG B 182 1 O ARG B 182 N TYR B 149 LINK C MSE A 22 N GLN A 23 1555 1555 1.33 LINK C ASP A 42 N MSE A 43 1555 1555 1.31 LINK C MSE A 43 N ASN A 44 1555 1555 1.33 LINK C GLU A 134 N MSE A 135 1555 1555 1.34 LINK C MSE A 135 N LYS A 136 1555 1555 1.34 LINK C LYS A 173 N MSE A 174 1555 1555 1.33 LINK C MSE A 174 N GLU A 175 1555 1555 1.33 LINK C ASN B 127 N MSE B 128 1555 1555 1.33 LINK C MSE B 128 N PHE B 129 1555 1555 1.32 LINK N MSE A 22 ZN ZN B 301 1555 3565 2.03 LINK O MSE A 22 ZN ZN B 301 1555 3565 1.88 LINK NE2 HIS B 49 ZN ZN B 301 1555 1555 2.27 LINK OE1 GLU B 65 ZN ZN B 301 1555 1555 2.11 LINK ND1 HIS B 133 ZN ZN B 301 1555 1555 2.27 CRYST1 105.185 105.185 154.771 90.00 90.00 120.00 P 65 2 2 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 0.009507 0.005489 0.000000 0.00000 SCALE2 0.000000 0.010978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006461 0.00000 HETATM 1 N MSE A 22 7.258 19.705 74.356 1.00 80.70 N ANISOU 1 N MSE A 22 6757 9173 14732 -224 523 -175 N HETATM 2 CA MSE A 22 8.673 19.389 74.365 1.00 79.40 C ANISOU 2 CA MSE A 22 6764 9173 14231 -205 635 -260 C HETATM 3 C MSE A 22 9.436 20.313 73.410 1.00 78.93 C ANISOU 3 C MSE A 22 6874 9272 13843 -268 480 -298 C HETATM 4 O MSE A 22 8.861 21.214 72.807 1.00 79.53 O ANISOU 4 O MSE A 22 6931 9338 13949 -320 299 -262 O HETATM 5 CB MSE A 22 8.899 17.916 74.004 1.00 80.70 C ANISOU 5 CB MSE A 22 6948 9306 14409 -233 644 -369 C HETATM 6 CG MSE A 22 9.003 17.608 72.513 1.00 86.40 C ANISOU 6 CG MSE A 22 7784 10051 14993 -354 386 -473 C HETATM 7 SE MSE A 22 9.771 15.834 72.115 1.00132.83 SE ANISOU 7 SE MSE A 22 13765 15943 20760 -382 461 -611 SE HETATM 8 CE MSE A 22 10.004 16.022 70.168 1.00 97.04 C ANISOU 8 CE MSE A 22 9446 11452 15974 -528 113 -713 C