HEADER HYDROLASE/HYDROLASE INHIBITOR 05-OCT-17 6B88 TITLE E. COLI LEPB IN COMPLEX WITH GNE0775 ((4S,7S,10S)-10-((S)-4-AMINO-2- TITLE 2 (2-(4-(TERT-BUTYL)PHENYL)-4-METHYLPYRIMIDINE-5-CARBOXAMIDO)-N- TITLE 3 METHYLBUTANAMIDO)-16,26-BIS(2-AMINOETHOXY)-N-(2-IMINOETHYL)-7-METHYL- TITLE 4 6,9-DIOXO-5,8-DIAZA-1,2(1,3)-DIBENZENACYCLODECAPHANE-4-CARBOXAMIDE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIGNAL PEPTIDASE I; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SPASE I,LEADER PEPTIDASE I; COMPND 5 EC: 3.4.21.89; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: LEPB, B2568, JW2552; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIGNAL PEPTIDASE, SBDD, ANTIBIOTIC, HYDROLASE, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.MURRAY,L.ROUGE REVDAT 3 04-OCT-23 6B88 1 REMARK REVDAT 2 24-OCT-18 6B88 1 COMPND JRNL REVDAT 1 10-OCT-18 6B88 0 JRNL AUTH P.A.SMITH,M.F.T.KOEHLER,H.S.GIRGIS,D.YAN,Y.CHEN,Y.CHEN, JRNL AUTH 2 J.J.CRAWFORD,M.R.DURK,R.I.HIGUCHI,J.KANG,J.MURRAY, JRNL AUTH 3 P.PARASELLI,S.PARK,W.PHUNG,J.G.QUINN,T.C.ROBERTS,L.ROUGE, JRNL AUTH 4 J.B.SCHWARZ,E.SKIPPINGTON,J.WAI,M.XU,Z.YU,H.ZHANG,M.W.TAN, JRNL AUTH 5 C.E.HEISE JRNL TITL OPTIMIZED ARYLOMYCINS ARE A NEW CLASS OF GRAM-NEGATIVE JRNL TITL 2 ANTIBIOTICS. JRNL REF NATURE V. 561 189 2018 JRNL REFN ESSN 1476-4687 JRNL PMID 30209367 JRNL DOI 10.1038/S41586-018-0483-6 REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 26558 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1349 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 55.0043 - 5.1847 0.99 2581 139 0.2374 0.2222 REMARK 3 2 5.1847 - 4.1156 0.99 2582 99 0.1863 0.2142 REMARK 3 3 4.1156 - 3.5955 0.99 2490 151 0.2031 0.2033 REMARK 3 4 3.5955 - 3.2668 1.00 2552 134 0.2072 0.2792 REMARK 3 5 3.2668 - 3.0327 1.00 2527 126 0.2505 0.3116 REMARK 3 6 3.0327 - 2.8539 1.00 2502 146 0.2623 0.2652 REMARK 3 7 2.8539 - 2.7110 0.99 2519 161 0.2900 0.3277 REMARK 3 8 2.7110 - 2.5930 0.99 2522 120 0.3098 0.3524 REMARK 3 9 2.5930 - 2.4931 0.98 2478 137 0.3108 0.3430 REMARK 3 10 2.4931 - 2.4071 0.97 2456 136 0.3406 0.3442 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.43 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 77 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0631 44.7769 7.6418 REMARK 3 T TENSOR REMARK 3 T11: 0.2427 T22: 0.1441 REMARK 3 T33: 0.1778 T12: -0.0011 REMARK 3 T13: -0.0190 T23: 0.0032 REMARK 3 L TENSOR REMARK 3 L11: 4.0353 L22: 3.4655 REMARK 3 L33: 5.0769 L12: -0.5686 REMARK 3 L13: -0.2810 L23: -0.2680 REMARK 3 S TENSOR REMARK 3 S11: -0.0195 S12: -0.0713 S13: 0.0392 REMARK 3 S21: 0.2936 S22: 0.1399 S23: 0.2872 REMARK 3 S31: -0.0496 S32: -0.2228 S33: 0.0243 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9523 38.6691 18.7402 REMARK 3 T TENSOR REMARK 3 T11: 0.5108 T22: 0.8160 REMARK 3 T33: 0.7129 T12: 0.0879 REMARK 3 T13: 0.1148 T23: -0.0954 REMARK 3 L TENSOR REMARK 3 L11: 5.6846 L22: 2.9871 REMARK 3 L33: 4.8628 L12: -1.4125 REMARK 3 L13: -0.5206 L23: 0.2912 REMARK 3 S TENSOR REMARK 3 S11: -0.4285 S12: -0.6560 S13: 0.3229 REMARK 3 S21: 0.0361 S22: -0.0272 S23: 1.5869 REMARK 3 S31: -0.0875 S32: -1.6374 S33: -0.0039 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 181 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.5871 30.2038 15.5183 REMARK 3 T TENSOR REMARK 3 T11: 0.4794 T22: 0.3062 REMARK 3 T33: 0.1428 T12: 0.1812 REMARK 3 T13: 0.0300 T23: -0.0370 REMARK 3 L TENSOR REMARK 3 L11: 4.2899 L22: 3.5938 REMARK 3 L33: 4.8481 L12: -0.8822 REMARK 3 L13: 0.2667 L23: 0.3837 REMARK 3 S TENSOR REMARK 3 S11: 0.3743 S12: -0.7743 S13: -0.6283 REMARK 3 S21: 0.6349 S22: -0.6070 S23: -0.1835 REMARK 3 S31: 1.2392 S32: 0.0516 S33: -0.1121 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 182 THROUGH 203 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.8854 35.7028 -1.7453 REMARK 3 T TENSOR REMARK 3 T11: 0.3872 T22: 0.8900 REMARK 3 T33: 0.4599 T12: 0.0292 REMARK 3 T13: 0.0084 T23: -0.1893 REMARK 3 L TENSOR REMARK 3 L11: 2.9271 L22: 3.4089 REMARK 3 L33: 4.4971 L12: -0.6464 REMARK 3 L13: 0.1060 L23: -0.3811 REMARK 3 S TENSOR REMARK 3 S11: 0.2698 S12: 0.8776 S13: 0.0017 REMARK 3 S21: 0.4194 S22: 0.1907 S23: -1.2112 REMARK 3 S31: -0.1288 S32: 1.3694 S33: -0.1213 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 204 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5302 38.1251 -5.5013 REMARK 3 T TENSOR REMARK 3 T11: 0.3644 T22: 1.0380 REMARK 3 T33: -0.0014 T12: -0.0060 REMARK 3 T13: 0.1829 T23: -0.2816 REMARK 3 L TENSOR REMARK 3 L11: 3.8275 L22: 4.0495 REMARK 3 L33: 4.3233 L12: 0.5842 REMARK 3 L13: -0.1345 L23: -0.3126 REMARK 3 S TENSOR REMARK 3 S11: -0.5099 S12: 2.1473 S13: 0.3402 REMARK 3 S21: 0.1643 S22: -0.2290 S23: -2.2920 REMARK 3 S31: -0.3541 S32: 1.9021 S33: -0.0669 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 231 THROUGH 268 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6006 29.8897 14.4384 REMARK 3 T TENSOR REMARK 3 T11: 0.5123 T22: 0.3577 REMARK 3 T33: 0.2813 T12: 0.2117 REMARK 3 T13: -0.0689 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 2.8402 L22: 2.5304 REMARK 3 L33: 4.5175 L12: -0.7551 REMARK 3 L13: 0.2183 L23: 0.0213 REMARK 3 S TENSOR REMARK 3 S11: -0.2279 S12: -0.2292 S13: -0.3842 REMARK 3 S21: 0.3800 S22: 0.2522 S23: -0.3316 REMARK 3 S31: 0.8201 S32: 0.4830 S33: -0.1282 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 269 THROUGH 323 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2919 40.7123 6.8773 REMARK 3 T TENSOR REMARK 3 T11: 0.1995 T22: 0.1939 REMARK 3 T33: 0.1600 T12: 0.0127 REMARK 3 T13: 0.0162 T23: -0.0534 REMARK 3 L TENSOR REMARK 3 L11: 3.3629 L22: 2.4958 REMARK 3 L33: 4.2026 L12: -1.4876 REMARK 3 L13: 1.2603 L23: -0.2623 REMARK 3 S TENSOR REMARK 3 S11: -0.0256 S12: 0.2069 S13: -0.0144 REMARK 3 S21: 0.1105 S22: 0.0973 S23: -0.1048 REMARK 3 S31: 0.4047 S32: 0.3123 S33: -0.0226 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 77 THROUGH 158 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7913 40.0486 -19.1429 REMARK 3 T TENSOR REMARK 3 T11: 0.2851 T22: 0.2512 REMARK 3 T33: 0.1758 T12: -0.0700 REMARK 3 T13: 0.0264 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 1.9902 L22: 3.2302 REMARK 3 L33: 4.6541 L12: -0.5449 REMARK 3 L13: 0.8922 L23: 0.9564 REMARK 3 S TENSOR REMARK 3 S11: -0.0269 S12: 0.3041 S13: 0.1520 REMARK 3 S21: -0.3658 S22: 0.0757 S23: -0.3772 REMARK 3 S31: 0.1532 S32: 0.3816 S33: -0.0504 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 159 THROUGH 201 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.0225 25.3831 -12.7194 REMARK 3 T TENSOR REMARK 3 T11: 0.6638 T22: 0.4008 REMARK 3 T33: 0.3123 T12: -0.2020 REMARK 3 T13: -0.1606 T23: 0.0702 REMARK 3 L TENSOR REMARK 3 L11: 3.4026 L22: 3.6568 REMARK 3 L33: 5.5972 L12: 0.8422 REMARK 3 L13: 0.1927 L23: 0.0888 REMARK 3 S TENSOR REMARK 3 S11: 0.0708 S12: -0.1126 S13: -0.6152 REMARK 3 S21: -0.5770 S22: -0.0672 S23: 0.6107 REMARK 3 S31: 0.9516 S32: -0.1913 S33: -0.0297 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 202 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.5418 35.4589 -0.9993 REMARK 3 T TENSOR REMARK 3 T11: 0.4041 T22: 0.7032 REMARK 3 T33: 0.3893 T12: -0.2912 REMARK 3 T13: -0.0455 T23: -0.0508 REMARK 3 L TENSOR REMARK 3 L11: 3.3221 L22: 3.9937 REMARK 3 L33: 4.8728 L12: -0.6356 REMARK 3 L13: -0.8398 L23: 0.8637 REMARK 3 S TENSOR REMARK 3 S11: -0.0761 S12: -0.8322 S13: -0.2213 REMARK 3 S21: 0.7440 S22: -0.1477 S23: 1.0088 REMARK 3 S31: 0.7296 S32: -1.1398 S33: 0.0224 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 231 THROUGH 280 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.9113 28.7082 -19.2731 REMARK 3 T TENSOR REMARK 3 T11: 0.5074 T22: 0.3039 REMARK 3 T33: 0.3007 T12: -0.2023 REMARK 3 T13: -0.0540 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 1.8595 L22: 2.3805 REMARK 3 L33: 4.7193 L12: 0.5169 REMARK 3 L13: -0.2703 L23: 0.5914 REMARK 3 S TENSOR REMARK 3 S11: -0.1277 S12: 0.0824 S13: -0.2289 REMARK 3 S21: -0.3709 S22: 0.0185 S23: 0.4422 REMARK 3 S31: 0.7645 S32: -0.5776 S33: -0.0106 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 281 THROUGH 323 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2272 41.5708 -11.9175 REMARK 3 T TENSOR REMARK 3 T11: 0.1953 T22: 0.2406 REMARK 3 T33: 0.1901 T12: -0.0786 REMARK 3 T13: 0.0048 T23: 0.0324 REMARK 3 L TENSOR REMARK 3 L11: 1.5132 L22: 2.0757 REMARK 3 L33: 4.7420 L12: 0.9020 REMARK 3 L13: 0.8999 L23: 0.9137 REMARK 3 S TENSOR REMARK 3 S11: -0.1584 S12: -0.0916 S13: -0.0698 REMARK 3 S21: 0.0460 S22: -0.0118 S23: -0.0302 REMARK 3 S31: 0.2616 S32: -0.1501 S33: -0.0316 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 77 THROUGH 114 OR REMARK 3 RESID 116 THROUGH 204 OR (RESID 205 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR REMARK 3 NAME CB )) OR RESID 206 THROUGH 302 OR REMARK 3 RESID 304 THROUGH 322)) REMARK 3 SELECTION : (CHAIN B AND (RESID 77 OR (RESID 78 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR REMARK 3 NAME CB )) OR RESID 79 THROUGH 114 OR REMARK 3 RESID 116 THROUGH 120 OR (RESID 121 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR REMARK 3 NAME CB )) OR RESID 122 THROUGH 176 OR REMARK 3 (RESID 177 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 178 REMARK 3 THROUGH 197 OR (RESID 198 THROUGH 200 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR REMARK 3 NAME CB )) OR RESID 201 THROUGH 202 OR REMARK 3 (RESID 203 THROUGH 205 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 206 THROUGH 302 OR RESID 304 OR REMARK 3 RESID 313 THROUGH 322)) REMARK 3 ATOM PAIRS NUMBER : 2224 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6B88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230366. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27848 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.372 REMARK 200 RESOLUTION RANGE LOW (A) : 79.969 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.19900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 1.30400 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: 1T7D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 300, 0.1 M SODIUM ACETATE PH REMARK 280 4.5, VAPOR DIFFUSION, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 54.99000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.99000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.12500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 54.99000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.99000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.12500 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 54.99000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 54.99000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 58.12500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 54.99000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 54.99000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 58.12500 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 305 REMARK 465 GLN A 306 REMARK 465 GLU A 307 REMARK 465 GLY A 308 REMARK 465 GLU A 309 REMARK 465 TRP A 310 REMARK 465 PRO A 311 REMARK 465 THR A 312 REMARK 465 GLN B 306 REMARK 465 GLU B 307 REMARK 465 GLY B 308 REMARK 465 GLU B 309 REMARK 465 TRP B 310 REMARK 465 PRO B 311 REMARK 465 THR B 312 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 SER A 78 OG REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 ASP A 112 CG OD1 OD2 REMARK 470 ILE A 114 CG1 CG2 CD1 REMARK 470 TYR A 115 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 116 CG CD OE1 NE2 REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 GLU A 121 CG CD OE1 OE2 REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 ARG A 198 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 199 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 200 CG OD1 ND2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 LYS B 111 CG CD CE NZ REMARK 470 ASP B 112 CG OD1 OD2 REMARK 470 ILE B 114 CG1 CG2 CD1 REMARK 470 TYR B 115 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN B 116 CG CD OE1 NE2 REMARK 470 LYS B 117 CG CD CE NZ REMARK 470 THR B 205 OG1 CG2 REMARK 470 LYS B 305 CG CD CE NZ 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 NZ LYS B 145 C44 CZD B 402 1.61 REMARK 500 NZ LYS A 145 C43 CZD A 401 2.10 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 ILE A 114 -72.89 -110.45 REMARK 500 TYR A 115 111.21 -161.79 REMARK 500 GLN A 116 -52.06 -154.81 REMARK 500 ASP A 138 87.22 -160.77 REMARK 500 CYS A 170 52.38 -101.03 REMARK 500 ASP A 280 -161.13 -120.80 REMARK 500 ILE B 114 -78.79 -104.78 REMARK 500 TYR B 115 112.22 -164.59 REMARK 500 GLN B 116 -52.66 -154.01 REMARK 500 CYS B 170 52.59 -100.73 REMARK 500 ASP B 280 -160.47 -122.06 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 B 548 DISTANCE = 6.39 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CZD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CZD B 402 DBREF 6B88 A 77 323 UNP P00803 LEP_ECOLI 78 324 DBREF 6B88 B 77 323 UNP P00803 LEP_ECOLI 78 324 SEQRES 1 A 247 ARG SER PHE ILE TYR GLU PRO PHE GLN ILE PRO SER GLY SEQRES 2 A 247 SER MET MET PRO THR LEU LEU ILE GLY ASP PHE ILE LEU SEQRES 3 A 247 VAL GLU LYS PHE ALA TYR GLY ILE LYS ASP PRO ILE TYR SEQRES 4 A 247 GLN LYS THR LEU ILE GLU THR GLY HIS PRO LYS ARG GLY SEQRES 5 A 247 ASP ILE VAL VAL PHE LYS TYR PRO GLU ASP PRO LYS LEU SEQRES 6 A 247 ASP TYR ILE LYS ARG ALA VAL GLY LEU PRO GLY ASP LYS SEQRES 7 A 247 VAL THR TYR ASP PRO VAL SER LYS GLU LEU THR ILE GLN SEQRES 8 A 247 PRO GLY CYS SER SER GLY GLN ALA CYS GLU ASN ALA LEU SEQRES 9 A 247 PRO VAL THR TYR SER ASN VAL GLU PRO SER ASP PHE VAL SEQRES 10 A 247 GLN THR PHE SER ARG ARG ASN GLY GLY GLU ALA THR SER SEQRES 11 A 247 GLY PHE PHE GLU VAL PRO LYS ASN GLU THR LYS GLU ASN SEQRES 12 A 247 GLY ILE ARG LEU SER GLU ARG LYS GLU THR LEU GLY ASP SEQRES 13 A 247 VAL THR HIS ARG ILE LEU THR VAL PRO ILE ALA GLN ASP SEQRES 14 A 247 GLN VAL GLY MET TYR TYR GLN GLN PRO GLY GLN GLN LEU SEQRES 15 A 247 ALA THR TRP ILE VAL PRO PRO GLY GLN TYR PHE MET MET SEQRES 16 A 247 GLY ASP ASN ARG ASP ASN SER ALA ASP SER ARG TYR TRP SEQRES 17 A 247 GLY PHE VAL PRO GLU ALA ASN LEU VAL GLY ARG ALA THR SEQRES 18 A 247 ALA ILE TRP MET SER PHE ASP LYS GLN GLU GLY GLU TRP SEQRES 19 A 247 PRO THR GLY LEU ARG LEU SER ARG ILE GLY GLY ILE HIS SEQRES 1 B 247 ARG SER PHE ILE TYR GLU PRO PHE GLN ILE PRO SER GLY SEQRES 2 B 247 SER MET MET PRO THR LEU LEU ILE GLY ASP PHE ILE LEU SEQRES 3 B 247 VAL GLU LYS PHE ALA TYR GLY ILE LYS ASP PRO ILE TYR SEQRES 4 B 247 GLN LYS THR LEU ILE GLU THR GLY HIS PRO LYS ARG GLY SEQRES 5 B 247 ASP ILE VAL VAL PHE LYS TYR PRO GLU ASP PRO LYS LEU SEQRES 6 B 247 ASP TYR ILE LYS ARG ALA VAL GLY LEU PRO GLY ASP LYS SEQRES 7 B 247 VAL THR TYR ASP PRO VAL SER LYS GLU LEU THR ILE GLN SEQRES 8 B 247 PRO GLY CYS SER SER GLY GLN ALA CYS GLU ASN ALA LEU SEQRES 9 B 247 PRO VAL THR TYR SER ASN VAL GLU PRO SER ASP PHE VAL SEQRES 10 B 247 GLN THR PHE SER ARG ARG ASN GLY GLY GLU ALA THR SER SEQRES 11 B 247 GLY PHE PHE GLU VAL PRO LYS ASN GLU THR LYS GLU ASN SEQRES 12 B 247 GLY ILE ARG LEU SER GLU ARG LYS GLU THR LEU GLY ASP SEQRES 13 B 247 VAL THR HIS ARG ILE LEU THR VAL PRO ILE ALA GLN ASP SEQRES 14 B 247 GLN VAL GLY MET TYR TYR GLN GLN PRO GLY GLN GLN LEU SEQRES 15 B 247 ALA THR TRP ILE VAL PRO PRO GLY GLN TYR PHE MET MET SEQRES 16 B 247 GLY ASP ASN ARG ASP ASN SER ALA ASP SER ARG TYR TRP SEQRES 17 B 247 GLY PHE VAL PRO GLU ALA ASN LEU VAL GLY ARG ALA THR SEQRES 18 B 247 ALA ILE TRP MET SER PHE ASP LYS GLN GLU GLY GLU TRP SEQRES 19 B 247 PRO THR GLY LEU ARG LEU SER ARG ILE GLY GLY ILE HIS HET CZD A 401 65 HET 1PE B 401 16 HET CZD B 402 65 HETNAM CZD (8S,11S,14S)-14-{[(2S)-4-AMINO-2-{[2-(4-TERT- HETNAM 2 CZD BUTYLPHENYL)-4-METHYLPYRIMIDINE-5- HETNAM 3 CZD CARBONYL]AMINO}BUTANOYL](METHYL)AMINO}-3,18-BIS(2- HETNAM 4 CZD AMINOETHOXY)-N-[(2Z)-2-IMINOETHYL]-11-METHYL-10,13- HETNAM 5 CZD DIOXO-9,12-DIAZATRICYCLO[13.3.1.1~2,6~]ICOSA-1(19), HETNAM 6 CZD 2(20),3,5,15,17-HEXAENE-8-CARBOXAMIDE HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 3 CZD 2(C47 H61 N11 O7) FORMUL 4 1PE C10 H22 O6 FORMUL 6 HOH *99(H2 O) HELIX 1 AA1 GLN A 246 TYR A 250 5 5 HELIX 2 AA2 ASP A 280 GLY A 285 1 6 HELIX 3 AA3 GLN B 246 TYR B 250 5 5 HELIX 4 AA4 ASP B 280 GLY B 285 1 6 SHEET 1 AA1 7 TYR A 81 GLN A 85 0 SHEET 2 AA1 7 ASP A 99 LYS A 105 -1 O ILE A 101 N PHE A 84 SHEET 3 AA1 7 LEU A 292 SER A 302 -1 O ARG A 295 N GLU A 104 SHEET 4 AA1 7 ILE A 130 LYS A 134 -1 N ILE A 130 O ALA A 296 SHEET 5 AA1 7 ASP A 142 GLY A 149 -1 O TYR A 143 N PHE A 133 SHEET 6 AA1 7 GLN A 267 MET A 271 -1 O MET A 271 N ARG A 146 SHEET 7 AA1 7 VAL A 287 PRO A 288 -1 O VAL A 287 N TYR A 268 SHEET 1 AA2 2 ALA A 107 LYS A 111 0 SHEET 2 AA2 2 THR A 118 THR A 122 -1 O LEU A 119 N ILE A 110 SHEET 1 AA3 3 GLU A 163 GLN A 167 0 SHEET 2 AA3 3 LYS A 154 ASP A 158 -1 N THR A 156 O THR A 165 SHEET 3 AA3 3 THR A 260 ILE A 262 -1 O TRP A 261 N VAL A 155 SHEET 1 AA4 4 VAL A 182 TYR A 184 0 SHEET 2 AA4 4 GLY A 220 LEU A 230 -1 O THR A 229 N THR A 183 SHEET 3 AA4 4 GLU A 188 SER A 197 -1 N GLN A 194 O ILE A 221 SHEET 4 AA4 4 ALA A 204 GLU A 210 -1 O ALA A 204 N SER A 197 SHEET 1 AA5 3 VAL A 182 TYR A 184 0 SHEET 2 AA5 3 GLY A 220 LEU A 230 -1 O THR A 229 N THR A 183 SHEET 3 AA5 3 VAL A 233 THR A 239 -1 O HIS A 235 N GLU A 228 SHEET 1 AA6 7 TYR B 81 ILE B 86 0 SHEET 2 AA6 7 ASP B 99 LYS B 105 -1 O ASP B 99 N ILE B 86 SHEET 3 AA6 7 LEU B 292 SER B 302 -1 O ARG B 295 N GLU B 104 SHEET 4 AA6 7 ILE B 130 LYS B 134 -1 N ILE B 130 O ALA B 296 SHEET 5 AA6 7 ASP B 142 GLY B 149 -1 O TYR B 143 N PHE B 133 SHEET 6 AA6 7 GLN B 267 MET B 271 -1 O MET B 271 N ARG B 146 SHEET 7 AA6 7 VAL B 287 PRO B 288 -1 O VAL B 287 N TYR B 268 SHEET 1 AA7 2 ALA B 107 LYS B 111 0 SHEET 2 AA7 2 THR B 118 THR B 122 -1 O LEU B 119 N ILE B 110 SHEET 1 AA8 3 GLU B 163 GLN B 167 0 SHEET 2 AA8 3 LYS B 154 ASP B 158 -1 N THR B 156 O THR B 165 SHEET 3 AA8 3 THR B 260 ILE B 262 -1 O TRP B 261 N VAL B 155 SHEET 1 AA9 4 VAL B 182 TYR B 184 0 SHEET 2 AA9 4 GLY B 220 LEU B 230 -1 O THR B 229 N THR B 183 SHEET 3 AA9 4 GLU B 188 SER B 197 -1 N GLU B 188 O GLU B 225 SHEET 4 AA9 4 ALA B 204 GLU B 210 -1 O ALA B 204 N SER B 197 SHEET 1 AB1 3 VAL B 182 TYR B 184 0 SHEET 2 AB1 3 GLY B 220 LEU B 230 -1 O THR B 229 N THR B 183 SHEET 3 AB1 3 VAL B 233 THR B 239 -1 O HIS B 235 N GLU B 228 SSBOND 1 CYS A 170 CYS A 176 1555 1555 2.03 SSBOND 2 CYS B 170 CYS B 176 1555 1555 2.04 LINK NZ LYS A 145 C44 CZD A 401 1555 1555 1.55 CISPEP 1 MET A 92 PRO A 93 0 2.93 CISPEP 2 MET B 92 PRO B 93 0 2.49 SITE 1 AC1 14 PRO A 83 PHE A 84 GLN A 85 PRO A 87 SITE 2 AC1 14 SER A 90 ASP A 142 TYR A 143 ILE A 144 SITE 3 AC1 14 LYS A 145 ALA A 279 TRP A 300 HOH A 522 SITE 4 AC1 14 LEU B 314 LEU B 316 SITE 1 AC2 9 TYR A 251 PRO A 254 TRP A 284 PHE A 286 SITE 2 AC2 9 GLU B 137 TYR B 251 GLN B 253 TRP B 284 SITE 3 AC2 9 HOH B 518 SITE 1 AC3 13 LEU A 314 GLU B 82 PRO B 83 PHE B 84 SITE 2 AC3 13 GLN B 85 PRO B 87 SER B 90 ASP B 142 SITE 3 AC3 13 TYR B 143 ILE B 144 LYS B 145 ALA B 279 SITE 4 AC3 13 TRP B 300 CRYST1 109.980 109.980 116.250 90.00 90.00 90.00 I 4 16 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 0.009093 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008602 0.00000