HEADER HYDROLASE 23-APR-15 5A0X TITLE SUBSTRATE PEPTIDE-BOUND STRUCTURE OF METALLOPROTEASE ZMP1 VARIANT TITLE 2 E143AY178F FROM CLOSTRIDIUM DIFFICILE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC METALLOPROTEASE ZMP1; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.24.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: WITHOUT SIGNAL PEPTIDE (MISSING AA 1-26), CLEAVED N- COMPND 8 TERMINAL HIS-TAG WITH THROMBIN, RESULTING GSH- OVERHANG; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SUBSTRATE PEPTIDE; COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM DIFFICILE; SOURCE 3 ORGANISM_TAXID: 272563; SOURCE 4 STRAIN: 630; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: CLOSTRIDIUM DIFFICILE; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE, METALLOPROTEASE, PROLINE SPECIFICITY EXPDTA X-RAY DIFFRACTION AUTHOR M.SCHACHERL,C.PICHLO,I.NEUNDORF,U.BAUMANN REVDAT 5 10-JAN-24 5A0X 1 REMARK LINK REVDAT 4 23-OCT-19 5A0X 1 ATOM REVDAT 3 06-MAR-19 5A0X 1 REMARK LINK REVDAT 2 16-SEP-15 5A0X 1 JRNL REVDAT 1 05-AUG-15 5A0X 0 JRNL AUTH M.SCHACHERL,C.PICHLO,I.NEUNDORF,U.BAUMANN JRNL TITL STRUCTURAL BASIS OF PROLINE-PROLINE PEPTIDE BOND SPECIFICITY JRNL TITL 2 OF THE METALLOPROTEASE ZMP1 IMPLICATED IN MOTILITY OF JRNL TITL 3 CLOSTRIDIUM DIFFICILE. JRNL REF STRUCTURE V. 23 1632 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 26211609 JRNL DOI 10.1016/J.STR.2015.06.018 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 43067 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) : 0.180 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2152 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 40.8615 - 4.1912 0.99 2832 150 0.1581 0.1672 REMARK 3 2 4.1912 - 3.3271 0.99 2760 144 0.1597 0.2072 REMARK 3 3 3.3271 - 2.9067 1.00 2755 145 0.1853 0.2054 REMARK 3 4 2.9067 - 2.6410 0.99 2728 144 0.1838 0.2000 REMARK 3 5 2.6410 - 2.4517 1.00 2722 143 0.1785 0.1998 REMARK 3 6 2.4517 - 2.3072 1.00 2749 145 0.1782 0.2125 REMARK 3 7 2.3072 - 2.1916 1.00 2681 141 0.1730 0.2222 REMARK 3 8 2.1916 - 2.0963 1.00 2737 144 0.1843 0.2020 REMARK 3 9 2.0963 - 2.0156 0.99 2724 143 0.1911 0.2542 REMARK 3 10 2.0156 - 1.9460 1.00 2686 142 0.2026 0.2534 REMARK 3 11 1.9460 - 1.8852 1.00 2721 142 0.2022 0.2119 REMARK 3 12 1.8852 - 1.8313 1.00 2722 143 0.2086 0.2145 REMARK 3 13 1.8313 - 1.7831 1.00 2686 142 0.2069 0.2336 REMARK 3 14 1.7831 - 1.7396 0.99 2735 143 0.2110 0.2641 REMARK 3 15 1.7396 - 1.7000 1.00 2677 141 0.2134 0.2499 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.02 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 3212 REMARK 3 ANGLE : 0.932 4352 REMARK 3 CHIRALITY : 0.038 475 REMARK 3 PLANARITY : 0.005 570 REMARK 3 DIHEDRAL : 11.710 1178 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 18 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.1066 -1.2653 244.5886 REMARK 3 T TENSOR REMARK 3 T11: 0.2366 T22: 0.1663 REMARK 3 T33: 0.1630 T12: -0.0062 REMARK 3 T13: 0.0632 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 7.6940 L22: 7.9628 REMARK 3 L33: 6.8036 L12: -1.2576 REMARK 3 L13: -2.0868 L23: 0.7366 REMARK 3 S TENSOR REMARK 3 S11: 0.0636 S12: 0.4201 S13: 0.3213 REMARK 3 S21: -0.4641 S22: -0.0379 S23: -0.7598 REMARK 3 S31: 0.1325 S32: 0.2785 S33: -0.0914 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.5509 7.9821 253.4372 REMARK 3 T TENSOR REMARK 3 T11: 0.1335 T22: 0.1332 REMARK 3 T33: 0.0845 T12: -0.0132 REMARK 3 T13: 0.0294 T23: 0.0193 REMARK 3 L TENSOR REMARK 3 L11: 1.2896 L22: 4.7517 REMARK 3 L33: 1.8651 L12: -0.6828 REMARK 3 L13: -0.3521 L23: 0.4119 REMARK 3 S TENSOR REMARK 3 S11: 0.0188 S12: 0.1605 S13: 0.1051 REMARK 3 S21: -0.0503 S22: -0.0355 S23: -0.1416 REMARK 3 S31: -0.1335 S32: 0.0758 S33: 0.0004 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 64 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.5716 -4.9608 248.9928 REMARK 3 T TENSOR REMARK 3 T11: 0.1737 T22: 0.1343 REMARK 3 T33: 0.1051 T12: -0.0111 REMARK 3 T13: 0.0171 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 1.1305 L22: 3.1923 REMARK 3 L33: 3.7735 L12: 1.0279 REMARK 3 L13: 0.5349 L23: 2.0281 REMARK 3 S TENSOR REMARK 3 S11: 0.1492 S12: 0.0884 S13: -0.0846 REMARK 3 S21: -0.4250 S22: -0.1420 S23: -0.0861 REMARK 3 S31: 0.1735 S32: -0.1282 S33: 0.0272 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 95 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.2278 5.5288 260.6143 REMARK 3 T TENSOR REMARK 3 T11: 0.0924 T22: 0.1407 REMARK 3 T33: 0.1790 T12: 0.0219 REMARK 3 T13: 0.0040 T23: 0.0227 REMARK 3 L TENSOR REMARK 3 L11: 6.3239 L22: 7.6322 REMARK 3 L33: 3.2155 L12: 4.0418 REMARK 3 L13: -2.1383 L23: -1.2143 REMARK 3 S TENSOR REMARK 3 S11: 0.0218 S12: 0.2271 S13: 0.1661 REMARK 3 S21: -0.0905 S22: 0.2176 S23: 0.1662 REMARK 3 S31: -0.3315 S32: -0.1448 S33: -0.1187 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 96 THROUGH 109 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.5731 -1.0706 272.9100 REMARK 3 T TENSOR REMARK 3 T11: 0.1482 T22: 0.1781 REMARK 3 T33: 0.1129 T12: -0.0151 REMARK 3 T13: 0.0397 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 4.0651 L22: 1.4895 REMARK 3 L33: 3.7200 L12: -1.2785 REMARK 3 L13: 0.1827 L23: 0.7519 REMARK 3 S TENSOR REMARK 3 S11: -0.0585 S12: -0.1291 S13: 0.1229 REMARK 3 S21: 0.2978 S22: 0.0977 S23: 0.1394 REMARK 3 S31: -0.1259 S32: -0.0527 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 110 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.4779 -0.6901 262.6846 REMARK 3 T TENSOR REMARK 3 T11: 0.0797 T22: 0.0901 REMARK 3 T33: 0.0799 T12: -0.0042 REMARK 3 T13: 0.0083 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.4798 L22: 2.4322 REMARK 3 L33: 1.5642 L12: -0.0943 REMARK 3 L13: -0.1884 L23: 0.2543 REMARK 3 S TENSOR REMARK 3 S11: 0.0534 S12: -0.1140 S13: 0.0540 REMARK 3 S21: 0.0543 S22: -0.0546 S23: -0.0011 REMARK 3 S31: -0.0425 S32: 0.0314 S33: -0.0173 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 152 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.2357 -20.5394 262.9014 REMARK 3 T TENSOR REMARK 3 T11: 0.2162 T22: 0.0884 REMARK 3 T33: 0.1267 T12: -0.0199 REMARK 3 T13: 0.0033 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 2.2678 L22: 1.8597 REMARK 3 L33: 5.2579 L12: 0.8124 REMARK 3 L13: 1.2435 L23: -0.4546 REMARK 3 S TENSOR REMARK 3 S11: 0.1741 S12: -0.0731 S13: -0.1928 REMARK 3 S21: 0.2875 S22: -0.0459 S23: -0.0033 REMARK 3 S31: 0.5103 S32: -0.0693 S33: -0.1599 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.8214 -12.5136 273.7324 REMARK 3 T TENSOR REMARK 3 T11: 0.2507 T22: 0.1479 REMARK 3 T33: 0.0895 T12: -0.0146 REMARK 3 T13: -0.0210 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 5.1251 L22: 2.2575 REMARK 3 L33: 2.4165 L12: -0.9885 REMARK 3 L13: 2.7994 L23: 0.4455 REMARK 3 S TENSOR REMARK 3 S11: -0.1217 S12: -0.0778 S13: -0.0023 REMARK 3 S21: 0.3768 S22: 0.0901 S23: -0.1018 REMARK 3 S31: -0.0283 S32: 0.0386 S33: 0.0384 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 183 THROUGH 220 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.1894 -13.2564 262.4751 REMARK 3 T TENSOR REMARK 3 T11: 0.1395 T22: 0.0971 REMARK 3 T33: 0.1317 T12: 0.0347 REMARK 3 T13: -0.0081 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 2.7682 L22: 2.0539 REMARK 3 L33: 1.6305 L12: 0.6933 REMARK 3 L13: -0.3801 L23: -0.2902 REMARK 3 S TENSOR REMARK 3 S11: -0.0362 S12: -0.0182 S13: -0.0582 REMARK 3 S21: 0.0555 S22: -0.0028 S23: -0.3328 REMARK 3 S31: 0.3593 S32: 0.2122 S33: 0.0208 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 30 THROUGH 63 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.9317 0.1058 299.2455 REMARK 3 T TENSOR REMARK 3 T11: 0.0999 T22: 0.1133 REMARK 3 T33: 0.1208 T12: 0.0222 REMARK 3 T13: 0.0172 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 2.1940 L22: 2.5013 REMARK 3 L33: 3.4712 L12: 0.1119 REMARK 3 L13: 0.2777 L23: -0.0362 REMARK 3 S TENSOR REMARK 3 S11: 0.0123 S12: 0.0059 S13: 0.0132 REMARK 3 S21: 0.0421 S22: -0.0037 S23: 0.1499 REMARK 3 S31: -0.3894 S32: -0.1253 S33: -0.0035 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 64 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.6861 -9.3470 303.5696 REMARK 3 T TENSOR REMARK 3 T11: 0.0896 T22: 0.1203 REMARK 3 T33: 0.0990 T12: 0.0021 REMARK 3 T13: 0.0140 T23: 0.0235 REMARK 3 L TENSOR REMARK 3 L11: 1.2613 L22: 3.4192 REMARK 3 L33: 3.3751 L12: 0.0442 REMARK 3 L13: -0.4785 L23: -2.5178 REMARK 3 S TENSOR REMARK 3 S11: 0.1684 S12: -0.2760 S13: -0.1045 REMARK 3 S21: 0.2369 S22: -0.2019 S23: 0.0651 REMARK 3 S31: 0.1950 S32: 0.0985 S33: 0.0335 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 83 THROUGH 95 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.4933 3.0237 299.0087 REMARK 3 T TENSOR REMARK 3 T11: 0.1678 T22: 0.1668 REMARK 3 T33: 0.1368 T12: -0.0626 REMARK 3 T13: 0.0167 T23: -0.0263 REMARK 3 L TENSOR REMARK 3 L11: 8.2536 L22: 7.1313 REMARK 3 L33: 2.7387 L12: -5.2559 REMARK 3 L13: 1.0063 L23: -1.7994 REMARK 3 S TENSOR REMARK 3 S11: 0.1264 S12: -0.2147 S13: 0.2586 REMARK 3 S21: 0.2417 S22: -0.0091 S23: -0.1053 REMARK 3 S31: -0.3043 S32: 0.4233 S33: -0.1295 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 96 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.7759 -4.3658 290.8847 REMARK 3 T TENSOR REMARK 3 T11: 0.1327 T22: 0.1345 REMARK 3 T33: 0.0960 T12: 0.0025 REMARK 3 T13: 0.0187 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 2.0914 L22: 1.5753 REMARK 3 L33: 1.0541 L12: 0.3251 REMARK 3 L13: -0.2113 L23: -0.1605 REMARK 3 S TENSOR REMARK 3 S11: 0.0246 S12: 0.0928 S13: 0.0365 REMARK 3 S21: -0.0921 S22: -0.0061 S23: -0.0523 REMARK 3 S31: -0.0008 S32: 0.1467 S33: -0.0103 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 152 THROUGH 195 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9775 -19.2387 287.6650 REMARK 3 T TENSOR REMARK 3 T11: 0.2248 T22: 0.1098 REMARK 3 T33: 0.1398 T12: 0.0082 REMARK 3 T13: -0.0096 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 2.4517 L22: 0.9061 REMARK 3 L33: 1.5163 L12: -0.2506 REMARK 3 L13: -0.2236 L23: -0.6386 REMARK 3 S TENSOR REMARK 3 S11: 0.1047 S12: 0.0910 S13: -0.2377 REMARK 3 S21: -0.1225 S22: -0.0766 S23: -0.0407 REMARK 3 S31: 0.0319 S32: 0.0874 S33: -0.0236 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 196 THROUGH 207 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.0527 -15.0768 281.6547 REMARK 3 T TENSOR REMARK 3 T11: 0.2661 T22: 0.1449 REMARK 3 T33: 0.1260 T12: -0.0087 REMARK 3 T13: -0.0438 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 3.0671 L22: 3.5393 REMARK 3 L33: 4.4757 L12: -2.4023 REMARK 3 L13: -0.4162 L23: 2.7177 REMARK 3 S TENSOR REMARK 3 S11: 0.1462 S12: 0.2507 S13: -0.0288 REMARK 3 S21: -0.4286 S22: -0.3430 S23: 0.2496 REMARK 3 S31: -0.1224 S32: -0.2373 S33: 0.0783 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 208 THROUGH 220 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.2237 -23.8152 289.5464 REMARK 3 T TENSOR REMARK 3 T11: 0.2737 T22: 0.1109 REMARK 3 T33: 0.1689 T12: -0.0275 REMARK 3 T13: -0.0549 T23: 0.0129 REMARK 3 L TENSOR REMARK 3 L11: 3.2922 L22: 2.9949 REMARK 3 L33: 9.0095 L12: 0.3292 REMARK 3 L13: -0.8833 L23: -0.8102 REMARK 3 S TENSOR REMARK 3 S11: 0.0743 S12: -0.1239 S13: -0.3208 REMARK 3 S21: 0.1956 S22: -0.0907 S23: 0.0898 REMARK 3 S31: 0.2666 S32: -0.2413 S33: 0.0240 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.5829 -4.4109 267.3745 REMARK 3 T TENSOR REMARK 3 T11: 0.1072 T22: 0.1410 REMARK 3 T33: 0.1315 T12: 0.0211 REMARK 3 T13: 0.0339 T23: 0.0127 REMARK 3 L TENSOR REMARK 3 L11: 6.1594 L22: 2.7649 REMARK 3 L33: 5.6558 L12: 0.9019 REMARK 3 L13: 4.8213 L23: 0.4566 REMARK 3 S TENSOR REMARK 3 S11: -0.0582 S12: 0.1940 S13: -0.2806 REMARK 3 S21: 0.2242 S22: 0.2252 S23: 0.1523 REMARK 3 S31: -0.3269 S32: -0.1382 S33: -0.0843 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 2 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.3257 -7.8124 289.2475 REMARK 3 T TENSOR REMARK 3 T11: 0.2792 T22: 0.1156 REMARK 3 T33: 0.1300 T12: 0.0329 REMARK 3 T13: 0.0669 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 4.6568 L22: 3.9474 REMARK 3 L33: 7.6444 L12: -1.0253 REMARK 3 L13: 3.0373 L23: -5.2475 REMARK 3 S TENSOR REMARK 3 S11: 0.0764 S12: -0.0366 S13: -0.0397 REMARK 3 S21: -0.2182 S22: 0.1024 S23: -0.1568 REMARK 3 S31: 0.0985 S32: 0.2817 S33: -0.0678 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5A0X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-15. REMARK 100 THE DEPOSITION ID IS D_1290063601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43083 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5800 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) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.780 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER IN REMARK 200 STARTING MODEL: PDB ENTRY 5A0P REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.25 AMMONIUM PHOSPHATE DIBASIC, 0.1 M REMARK 280 TRIS PH 9.0 GROWN AT 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.47050 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 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 GLY A 23 REMARK 465 SER A 24 REMARK 465 HIS A 25 REMARK 465 MET A 26 REMARK 465 GLY B 23 REMARK 465 SER B 24 REMARK 465 HIS B 25 REMARK 465 MET B 26 REMARK 465 ASP B 27 REMARK 465 SER B 28 REMARK 465 THR B 29 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 HOH A 2001 O HOH A 2009 2.11 REMARK 500 OD2 ASP A 88 O HOH A 2093 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2029 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A2107 DISTANCE = 5.85 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 AMIDATION (NH2): AMIDATION AT THE C-TERMINUS OF THE REMARK 600 SUBSTRATE PEPTIDE REMARK 600 ACETYLATION (ACE): ACETYLATION T THE N-TERMINUS OF THE REMARK 600 SUBSTRATE PEPTIDE 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 A1221 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 142 NE2 REMARK 620 2 HIS A 146 NE2 103.3 REMARK 620 3 GLU A 185 OE1 92.2 84.0 REMARK 620 4 PRO C 4 O 105.8 142.0 118.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1221 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 142 NE2 REMARK 620 2 HIS B 146 NE2 97.5 REMARK 620 3 GLU B 185 OE1 96.3 96.5 REMARK 620 4 PRO D 4 O 108.5 134.8 115.9 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 1221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1221 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A0P RELATED DB: PDB REMARK 900 APO-STRUCTURE OF METALLOPROTEASE ZMP1 FROM CLOSTRIDIUM DIFFICILE REMARK 900 RELATED ID: 5A0R RELATED DB: PDB REMARK 900 PRODUCT PEPTIDE-BOUND STRUCTURE OF METALLOPROTEASE ZMP1 VARIANT REMARK 900 E143A FROM CLOSTRIDIUM DIFFICILE REMARK 900 RELATED ID: 5A0S RELATED DB: PDB REMARK 900 APO-STRUCTURE OF METALLOPROTEASE ZMP1 VARIANT E143A FROM REMARK 900 CLOSTRIDIUM DIFFICILE DBREF 5A0X A 27 220 UNP Q183R7 ZMP1_PEPD6 27 220 DBREF 5A0X B 27 220 UNP Q183R7 ZMP1_PEPD6 27 220 DBREF 5A0X C 0 8 PDB 5A0X 5A0X 0 8 DBREF 5A0X D 0 8 PDB 5A0X 5A0X 0 8 SEQADV 5A0X GLY A 23 UNP Q183R7 EXPRESSION TAG SEQADV 5A0X SER A 24 UNP Q183R7 EXPRESSION TAG SEQADV 5A0X HIS A 25 UNP Q183R7 EXPRESSION TAG SEQADV 5A0X MET A 26 UNP Q183R7 EXPRESSION TAG SEQADV 5A0X ALA A 143 UNP Q183R7 GLU 143 ENGINEERED MUTATION SEQADV 5A0X PHE A 178 UNP Q183R7 TYR 178 ENGINEERED MUTATION SEQADV 5A0X GLY B 23 UNP Q183R7 EXPRESSION TAG SEQADV 5A0X SER B 24 UNP Q183R7 EXPRESSION TAG SEQADV 5A0X HIS B 25 UNP Q183R7 EXPRESSION TAG SEQADV 5A0X MET B 26 UNP Q183R7 EXPRESSION TAG SEQADV 5A0X ALA B 143 UNP Q183R7 GLU 143 ENGINEERED MUTATION SEQADV 5A0X PHE B 178 UNP Q183R7 TYR 178 ENGINEERED MUTATION SEQRES 1 A 198 GLY SER HIS MET ASP SER THR THR ILE GLN GLN ASN LYS SEQRES 2 A 198 ASP THR LEU SER GLN ILE VAL VAL PHE PRO THR GLY ASN SEQRES 3 A 198 TYR ASP LYS ASN GLU ALA ASN ALA MET VAL ASN ARG LEU SEQRES 4 A 198 ALA ASN ILE ASP GLY LYS TYR LEU ASN ALA LEU LYS GLN SEQRES 5 A 198 ASN ASN LEU LYS ILE LYS LEU LEU SER GLY LYS LEU THR SEQRES 6 A 198 ASP GLU LYS GLU TYR ALA TYR LEU LYS GLY VAL VAL PRO SEQRES 7 A 198 LYS GLY TRP GLU GLY THR GLY LYS THR TRP ASP ASP VAL SEQRES 8 A 198 PRO GLY LEU GLY GLY SER THR VAL ALA LEU ARG ILE GLY SEQRES 9 A 198 PHE SER ASN LYS GLY LYS GLY HIS ASP ALA ILE ASN LEU SEQRES 10 A 198 GLU LEU HIS ALA THR ALA HIS ALA ILE ASP HIS ILE VAL SEQRES 11 A 198 LEU ASN ASP ILE SER LYS SER ALA GLN PHE LYS GLN ILE SEQRES 12 A 198 PHE ALA LYS GLU GLY ARG SER LEU GLY ASN VAL ASN PHE SEQRES 13 A 198 LEU GLY VAL TYR PRO GLU GLU PHE PHE ALA GLU SER PHE SEQRES 14 A 198 ALA TYR TYR TYR LEU ASN GLN ASP THR ASN SER LYS LEU SEQRES 15 A 198 LYS SER ALA CYS PRO GLN THR TYR SER PHE LEU GLN ASN SEQRES 16 A 198 LEU ALA LYS SEQRES 1 B 198 GLY SER HIS MET ASP SER THR THR ILE GLN GLN ASN LYS SEQRES 2 B 198 ASP THR LEU SER GLN ILE VAL VAL PHE PRO THR GLY ASN SEQRES 3 B 198 TYR ASP LYS ASN GLU ALA ASN ALA MET VAL ASN ARG LEU SEQRES 4 B 198 ALA ASN ILE ASP GLY LYS TYR LEU ASN ALA LEU LYS GLN SEQRES 5 B 198 ASN ASN LEU LYS ILE LYS LEU LEU SER GLY LYS LEU THR SEQRES 6 B 198 ASP GLU LYS GLU TYR ALA TYR LEU LYS GLY VAL VAL PRO SEQRES 7 B 198 LYS GLY TRP GLU GLY THR GLY LYS THR TRP ASP ASP VAL SEQRES 8 B 198 PRO GLY LEU GLY GLY SER THR VAL ALA LEU ARG ILE GLY SEQRES 9 B 198 PHE SER ASN LYS GLY LYS GLY HIS ASP ALA ILE ASN LEU SEQRES 10 B 198 GLU LEU HIS ALA THR ALA HIS ALA ILE ASP HIS ILE VAL SEQRES 11 B 198 LEU ASN ASP ILE SER LYS SER ALA GLN PHE LYS GLN ILE SEQRES 12 B 198 PHE ALA LYS GLU GLY ARG SER LEU GLY ASN VAL ASN PHE SEQRES 13 B 198 LEU GLY VAL TYR PRO GLU GLU PHE PHE ALA GLU SER PHE SEQRES 14 B 198 ALA TYR TYR TYR LEU ASN GLN ASP THR ASN SER LYS LEU SEQRES 15 B 198 LYS SER ALA CYS PRO GLN THR TYR SER PHE LEU GLN ASN SEQRES 16 B 198 LEU ALA LYS SEQRES 1 C 9 ACE GLU VAL ASN PRO PRO VAL PRO NH2 SEQRES 1 D 9 ACE GLU VAL ASN PRO PRO VAL PRO NH2 HET ACE C 0 3 HET NH2 C 8 3 HET ACE D 0 3 HET NH2 D 8 3 HET ZN A1221 1 HET ZN B1221 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 NH2 2(H2 N) FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *428(H2 O) HELIX 1 1 ASP A 27 SER A 39 1 13 HELIX 2 2 ASP A 50 ALA A 62 1 13 HELIX 3 3 ASP A 65 ASN A 75 1 11 HELIX 4 4 LYS A 85 GLU A 89 5 5 HELIX 5 5 GLU A 89 LYS A 96 5 8 HELIX 6 6 THR A 109 VAL A 113 5 5 HELIX 7 7 ASN A 138 VAL A 152 1 15 HELIX 8 8 ASP A 155 LYS A 158 5 4 HELIX 9 9 SER A 159 GLY A 170 1 12 HELIX 10 10 TYR A 182 ASN A 197 1 16 HELIX 11 11 ASN A 197 CYS A 208 1 12 HELIX 12 12 CYS A 208 ALA A 219 1 12 HELIX 13 13 THR B 30 GLN B 40 1 11 HELIX 14 14 ASP B 50 ALA B 62 1 13 HELIX 15 15 ASP B 65 ASN B 75 1 11 HELIX 16 16 LYS B 85 GLU B 89 5 5 HELIX 17 17 GLU B 89 LYS B 96 5 8 HELIX 18 18 THR B 109 VAL B 113 5 5 HELIX 19 19 ASN B 138 VAL B 152 1 15 HELIX 20 20 ASP B 155 LYS B 158 5 4 HELIX 21 21 SER B 159 GLY B 170 1 12 HELIX 22 22 ASN B 175 GLY B 180 1 6 HELIX 23 23 TYR B 182 ASN B 197 1 16 HELIX 24 24 ASN B 197 CYS B 208 1 12 HELIX 25 25 CYS B 208 ALA B 219 1 12 SHEET 1 AA 5 VAL A 42 VAL A 43 0 SHEET 2 AA 5 ILE A 79 LEU A 82 1 O ILE A 79 N VAL A 43 SHEET 3 AA 5 VAL A 121 ARG A 124 1 O VAL A 121 N LYS A 80 SHEET 4 AA 5 GLY A 115 GLY A 118 -1 O LEU A 116 N ALA A 122 SHEET 5 AA 5 VAL C 2 ASN C 3 -1 O ASN C 3 N GLY A 117 SHEET 1 BA 5 VAL B 42 VAL B 43 0 SHEET 2 BA 5 ILE B 79 LEU B 82 1 O ILE B 79 N VAL B 43 SHEET 3 BA 5 VAL B 121 ARG B 124 1 O VAL B 121 N LYS B 80 SHEET 4 BA 5 GLY B 115 GLY B 118 -1 O LEU B 116 N ALA B 122 SHEET 5 BA 5 VAL D 2 ASN D 3 -1 O ASN D 3 N GLY B 117 LINK C ACE C 0 N GLU C 1 1555 1555 1.33 LINK C PRO C 7 N NH2 C 8 1555 1555 1.33 LINK C ACE D 0 N GLU D 1 1555 1555 1.34 LINK C PRO D 7 N NH2 D 8 1555 1555 1.33 LINK NE2 HIS A 142 ZN ZN A1221 1555 1555 2.03 LINK NE2 HIS A 146 ZN ZN A1221 1555 1555 2.24 LINK OE1 GLU A 185 ZN ZN A1221 1555 1555 1.98 LINK ZN ZN A1221 O PRO C 4 1555 1555 2.08 LINK NE2 HIS B 142 ZN ZN B1221 1555 1555 2.15 LINK NE2 HIS B 146 ZN ZN B1221 1555 1555 2.16 LINK OE1 GLU B 185 ZN ZN B1221 1555 1555 1.95 LINK ZN ZN B1221 O PRO D 4 1555 1555 2.07 SITE 1 AC1 4 HIS A 142 HIS A 146 GLU A 185 PRO C 4 SITE 1 AC2 4 HIS B 142 HIS B 146 GLU B 185 PRO D 4 CRYST1 37.435 42.941 123.244 90.00 96.09 90.00 P 1 21 1 4 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 0.026713 0.000000 0.002850 0.00000 SCALE2 0.000000 0.023288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008160 0.00000 MTRIX1 1 -0.877500 -0.095800 -0.470000 104.79870 1 MTRIX2 1 -0.098300 0.995000 -0.019100 8.89160 1 MTRIX3 1 0.469400 0.029400 -0.882500 522.65550 1