HEADER TRANSFERASE 15-SEP-11 4A1J TITLE YKUD L,D-TRANSPEPTIDASE FROM B.SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE L, D-TRANSPEPTIDASE YKUD; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: YKUD L\,D TRANSPEPTIDASE, SPORE PROTEIN YKUD; COMPND 5 EC: 2.-.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGS21A KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.BLAISE,S.FUGLSANG MIDTGAARD,S.ROI MIDTGAARD,T.BOESEN,S.THIRUP REVDAT 2 20-DEC-23 4A1J 1 REMARK REVDAT 1 26-SEP-12 4A1J 0 JRNL AUTH M.BLAISE,S.FUGLSANG MIDTGAARD,S.ROI MIDTGAARD,T.BOESEN, JRNL AUTH 2 S.THIRUP JRNL TITL STRUCTURE OF YKUD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 18627 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1862 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 47.1254 - 5.1711 0.99 1414 157 0.1580 0.1771 REMARK 3 2 5.1711 - 4.1052 1.00 1338 148 0.1256 0.1596 REMARK 3 3 4.1052 - 3.5865 0.98 1310 145 0.1602 0.2144 REMARK 3 4 3.5865 - 3.2587 1.00 1304 146 0.1692 0.2155 REMARK 3 5 3.2587 - 3.0251 1.00 1310 145 0.1841 0.2488 REMARK 3 6 3.0251 - 2.8468 1.00 1300 145 0.1954 0.2474 REMARK 3 7 2.8468 - 2.7042 1.00 1292 143 0.2029 0.2585 REMARK 3 8 2.7042 - 2.5865 1.00 1290 144 0.1998 0.2633 REMARK 3 9 2.5865 - 2.4870 1.00 1295 143 0.1888 0.3062 REMARK 3 10 2.4870 - 2.4012 1.00 1285 143 0.1853 0.2554 REMARK 3 11 2.4012 - 2.3261 1.00 1286 142 0.2052 0.2590 REMARK 3 12 2.3261 - 2.2596 0.88 1123 125 0.4279 0.5351 REMARK 3 13 2.2596 - 2.2001 0.94 1218 136 0.4363 0.4892 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 23.70 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.05280 REMARK 3 B22 (A**2) : 2.58230 REMARK 3 B33 (A**2) : 1.73760 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.008 2554 REMARK 3 ANGLE : 1.072 3486 REMARK 3 CHIRALITY : 0.072 406 REMARK 3 PLANARITY : 0.005 444 REMARK 3 DIHEDRAL : 12.917 922 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 0:29) REMARK 3 ORIGIN FOR THE GROUP (A): -12.5378 16.4547 -1.8673 REMARK 3 T TENSOR REMARK 3 T11: 0.0950 T22: 0.0740 REMARK 3 T33: 0.0853 T12: -0.0185 REMARK 3 T13: -0.0019 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.9134 L22: 1.3226 REMARK 3 L33: 1.9347 L12: 0.8044 REMARK 3 L13: -0.3730 L23: -0.0068 REMARK 3 S TENSOR REMARK 3 S11: -0.2189 S12: 0.0913 S13: -0.2328 REMARK 3 S21: -0.1164 S22: -0.0301 S23: -0.1481 REMARK 3 S31: 0.0527 S32: -0.0950 S33: -0.0109 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 30:41) REMARK 3 ORIGIN FOR THE GROUP (A): -8.7976 14.6306 6.6728 REMARK 3 T TENSOR REMARK 3 T11: 0.1499 T22: 0.1403 REMARK 3 T33: 0.1846 T12: 0.0363 REMARK 3 T13: -0.0638 T23: 0.0411 REMARK 3 L TENSOR REMARK 3 L11: 1.0688 L22: 0.7048 REMARK 3 L33: 0.6852 L12: 0.6157 REMARK 3 L13: -0.7279 L23: -0.1618 REMARK 3 S TENSOR REMARK 3 S11: -0.0646 S12: -0.0591 S13: -0.2231 REMARK 3 S21: 0.1813 S22: -0.2083 S23: -0.4196 REMARK 3 S31: -0.0121 S32: 0.3185 S33: -0.4292 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 42:61) REMARK 3 ORIGIN FOR THE GROUP (A): -26.5820 15.3025 -5.5686 REMARK 3 T TENSOR REMARK 3 T11: 0.0899 T22: 0.1000 REMARK 3 T33: 0.0667 T12: -0.0054 REMARK 3 T13: 0.0326 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 0.4824 L22: 0.1099 REMARK 3 L33: 0.9923 L12: 0.1580 REMARK 3 L13: 0.6591 L23: 0.2836 REMARK 3 S TENSOR REMARK 3 S11: 0.0213 S12: -0.1692 S13: 0.0133 REMARK 3 S21: -0.0371 S22: -0.0149 S23: -0.0510 REMARK 3 S31: -0.0805 S32: -0.3750 S33: 0.1023 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 62:92) REMARK 3 ORIGIN FOR THE GROUP (A): -27.1682 8.1999 -20.7412 REMARK 3 T TENSOR REMARK 3 T11: 0.0814 T22: 0.0747 REMARK 3 T33: 0.0938 T12: 0.0047 REMARK 3 T13: 0.0395 T23: -0.0229 REMARK 3 L TENSOR REMARK 3 L11: 1.8723 L22: 1.1146 REMARK 3 L33: 1.7880 L12: -0.5517 REMARK 3 L13: -0.6229 L23: 0.2977 REMARK 3 S TENSOR REMARK 3 S11: -0.0383 S12: 0.0397 S13: -0.1810 REMARK 3 S21: -0.1013 S22: 0.0079 S23: 0.0304 REMARK 3 S31: 0.0806 S32: -0.1201 S33: 0.0699 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 93:143) REMARK 3 ORIGIN FOR THE GROUP (A): -19.8984 17.1001 -22.0451 REMARK 3 T TENSOR REMARK 3 T11: 0.1085 T22: 0.0998 REMARK 3 T33: 0.1443 T12: 0.0022 REMARK 3 T13: 0.0642 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 1.2927 L22: 1.0408 REMARK 3 L33: 1.5628 L12: -0.1252 REMARK 3 L13: 0.4649 L23: 0.6457 REMARK 3 S TENSOR REMARK 3 S11: 0.0940 S12: 0.1724 S13: 0.2318 REMARK 3 S21: -0.2601 S22: 0.0569 S23: -0.0799 REMARK 3 S31: -0.3857 S32: 0.0390 S33: -0.0595 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 144:153) REMARK 3 ORIGIN FOR THE GROUP (A): -30.5839 21.1605 -23.0132 REMARK 3 T TENSOR REMARK 3 T11: 0.2562 T22: 0.1438 REMARK 3 T33: 0.1469 T12: 0.0435 REMARK 3 T13: 0.0186 T23: 0.0669 REMARK 3 L TENSOR REMARK 3 L11: 3.6393 L22: 1.5764 REMARK 3 L33: 3.3873 L12: -0.7212 REMARK 3 L13: -3.5067 L23: 0.5929 REMARK 3 S TENSOR REMARK 3 S11: 0.0671 S12: 0.4574 S13: -0.0727 REMARK 3 S21: -0.2727 S22: -0.1939 S23: 0.0193 REMARK 3 S31: 0.0522 S32: -0.2830 S33: -0.2905 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 154:164) REMARK 3 ORIGIN FOR THE GROUP (A): -25.8095 11.0420 -12.6694 REMARK 3 T TENSOR REMARK 3 T11: 0.0456 T22: 0.1975 REMARK 3 T33: 0.1120 T12: -0.0072 REMARK 3 T13: 0.0090 T23: 0.0435 REMARK 3 L TENSOR REMARK 3 L11: 2.0564 L22: 5.8102 REMARK 3 L33: 3.5507 L12: -0.8081 REMARK 3 L13: -0.3309 L23: 1.0174 REMARK 3 S TENSOR REMARK 3 S11: -0.0731 S12: -0.3482 S13: -0.2749 REMARK 3 S21: 0.0725 S22: -0.0950 S23: -0.0477 REMARK 3 S31: 0.3320 S32: 0.0510 S33: -0.1718 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 0:11) REMARK 3 ORIGIN FOR THE GROUP (A): -6.0871 38.8615 -16.1261 REMARK 3 T TENSOR REMARK 3 T11: 0.1632 T22: 0.1551 REMARK 3 T33: 0.2281 T12: 0.0189 REMARK 3 T13: -0.1468 T23: 0.0240 REMARK 3 L TENSOR REMARK 3 L11: 4.3482 L22: 1.3332 REMARK 3 L33: 2.2463 L12: -0.8186 REMARK 3 L13: 1.9419 L23: -0.7506 REMARK 3 S TENSOR REMARK 3 S11: -0.1022 S12: 0.1684 S13: 0.3249 REMARK 3 S21: -0.1447 S22: 0.0352 S23: 0.1288 REMARK 3 S31: -0.0698 S32: -0.1253 S33: 0.0716 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 12:29) REMARK 3 ORIGIN FOR THE GROUP (A): -11.7583 33.0601 -9.9616 REMARK 3 T TENSOR REMARK 3 T11: 0.0794 T22: 0.0189 REMARK 3 T33: 0.0830 T12: 0.0890 REMARK 3 T13: -0.0033 T23: -0.0578 REMARK 3 L TENSOR REMARK 3 L11: 0.9373 L22: 0.6818 REMARK 3 L33: 1.5633 L12: -0.1595 REMARK 3 L13: -0.7904 L23: 0.8455 REMARK 3 S TENSOR REMARK 3 S11: -0.0349 S12: 0.0205 S13: 0.1083 REMARK 3 S21: 0.2031 S22: -0.0047 S23: 0.1954 REMARK 3 S31: 0.0236 S32: -0.1467 S33: 0.0286 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 30:71) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2209 33.3634 -15.9256 REMARK 3 T TENSOR REMARK 3 T11: 0.0863 T22: 0.1156 REMARK 3 T33: 0.0507 T12: -0.0084 REMARK 3 T13: 0.0028 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 1.3036 L22: 0.8298 REMARK 3 L33: 0.8590 L12: -0.2597 REMARK 3 L13: -0.5467 L23: -0.1057 REMARK 3 S TENSOR REMARK 3 S11: -0.0999 S12: -0.0018 S13: 0.2408 REMARK 3 S21: 0.1200 S22: 0.0832 S23: -0.0435 REMARK 3 S31: -0.0452 S32: 0.0076 S33: -0.0485 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 72:80) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5854 23.1038 -21.4974 REMARK 3 T TENSOR REMARK 3 T11: 0.1697 T22: 0.2685 REMARK 3 T33: 0.2264 T12: -0.0068 REMARK 3 T13: -0.0249 T23: -0.0417 REMARK 3 L TENSOR REMARK 3 L11: 3.7660 L22: 5.5838 REMARK 3 L33: 2.5886 L12: 3.7611 REMARK 3 L13: 2.5448 L23: 2.8675 REMARK 3 S TENSOR REMARK 3 S11: 0.0604 S12: 0.2068 S13: 0.5084 REMARK 3 S21: -0.0619 S22: -0.0510 S23: -0.1302 REMARK 3 S31: 0.1503 S32: 0.1994 S33: -0.1220 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 81:92) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4730 21.5728 -31.3368 REMARK 3 T TENSOR REMARK 3 T11: 0.2922 T22: 0.3580 REMARK 3 T33: 0.2506 T12: -0.0122 REMARK 3 T13: -0.0695 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 2.4229 L22: 2.6224 REMARK 3 L33: 0.6188 L12: 1.1299 REMARK 3 L13: 0.3874 L23: 0.5689 REMARK 3 S TENSOR REMARK 3 S11: -0.2209 S12: 0.6102 S13: -0.0218 REMARK 3 S21: -0.7559 S22: 0.2282 S23: 0.6843 REMARK 3 S31: -0.1477 S32: -0.3791 S33: 0.1124 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 93:120) REMARK 3 ORIGIN FOR THE GROUP (A): -2.6324 19.9753 -15.9359 REMARK 3 T TENSOR REMARK 3 T11: 0.1141 T22: 0.1379 REMARK 3 T33: 0.1358 T12: 0.0008 REMARK 3 T13: -0.0052 T23: -0.0279 REMARK 3 L TENSOR REMARK 3 L11: 2.0473 L22: 2.8594 REMARK 3 L33: 1.5696 L12: 0.4466 REMARK 3 L13: -0.0218 L23: 0.6676 REMARK 3 S TENSOR REMARK 3 S11: 0.1812 S12: 0.0072 S13: -0.1591 REMARK 3 S21: 0.1648 S22: -0.2167 S23: -0.0180 REMARK 3 S31: 0.0620 S32: -0.3169 S33: -0.0171 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN B AND (RESSEQ 121:164) REMARK 3 ORIGIN FOR THE GROUP (A): 2.8759 17.3258 -22.2084 REMARK 3 T TENSOR REMARK 3 T11: 0.1225 T22: 0.1545 REMARK 3 T33: 0.1511 T12: 0.0237 REMARK 3 T13: 0.0195 T23: -0.0752 REMARK 3 L TENSOR REMARK 3 L11: 0.8521 L22: 1.8708 REMARK 3 L33: 1.1716 L12: 0.0247 REMARK 3 L13: 0.0464 L23: 0.0689 REMARK 3 S TENSOR REMARK 3 S11: -0.0279 S12: 0.1918 S13: -0.2283 REMARK 3 S21: -0.0658 S22: -0.0495 S23: -0.2100 REMARK 3 S31: 0.0832 S32: -0.1518 S33: -0.0184 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 4A1J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1290049672. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18649 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 74.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.7 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1Y7M REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS PH 5.5, 200 MM AMSO4, REMARK 280 25 % PEG 3350 AND 2 MM MURNAC MONOSACCHARIDE. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 28.12000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.12000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.14000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -111.6 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 117 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLN 118 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 117 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, GLN 118 TO ALA 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 MET B 76 SD 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 SER A 116 31.19 -77.18 REMARK 500 THR A 125 146.92 -173.01 REMARK 500 LYS B 85 175.87 -56.77 REMARK 500 SER B 116 42.26 -78.67 REMARK 500 HIS B 119 -3.47 80.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 SO4 B 1168 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1166 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1166 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1167 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1168 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y7M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE B. SUBTILIS YKUD PROTEIN AT 2 ARESOLUTION REMARK 900 RELATED ID: 3ZQD RELATED DB: PDB REMARK 900 B. SUBTILIS L,D-TRANSPEPTIDASE REMARK 900 RELATED ID: 4A1I RELATED DB: PDB REMARK 900 YKUD FROM B.SUBTILIS REMARK 900 RELATED ID: 4A1K RELATED DB: PDB REMARK 900 YKUD L,D-TRANSPEPTIDASE DBREF 4A1J A 1 164 UNP O34816 YKUD_BACSU 1 164 DBREF 4A1J B 1 164 UNP O34816 YKUD_BACSU 1 164 SEQADV 4A1J GLY A 0 UNP O34816 EXPRESSION TAG SEQADV 4A1J ALA A 117 UNP O34816 LYS 117 ENGINEERED MUTATION SEQADV 4A1J ALA A 118 UNP O34816 GLN 118 ENGINEERED MUTATION SEQADV 4A1J GLY B 0 UNP O34816 EXPRESSION TAG SEQADV 4A1J ALA B 117 UNP O34816 LYS 117 ENGINEERED MUTATION SEQADV 4A1J ALA B 118 UNP O34816 GLN 118 ENGINEERED MUTATION SEQRES 1 A 165 GLY MET LEU THR TYR GLN VAL LYS GLN GLY ASP THR LEU SEQRES 2 A 165 ASN SER ILE ALA ALA ASP PHE ARG ILE SER THR ALA ALA SEQRES 3 A 165 LEU LEU GLN ALA ASN PRO SER LEU GLN ALA GLY LEU THR SEQRES 4 A 165 ALA GLY GLN SER ILE VAL ILE PRO GLY LEU PRO ASP PRO SEQRES 5 A 165 TYR THR ILE PRO TYR HIS ILE ALA VAL SER ILE GLY ALA SEQRES 6 A 165 LYS THR LEU THR LEU SER LEU ASN ASN ARG VAL MET LYS SEQRES 7 A 165 THR TYR PRO ILE ALA VAL GLY LYS ILE LEU THR GLN THR SEQRES 8 A 165 PRO THR GLY GLU PHE TYR ILE ILE ASN ARG GLN ARG ASN SEQRES 9 A 165 PRO GLY GLY PRO PHE GLY ALA TYR TRP LEU SER LEU SER SEQRES 10 A 165 ALA ALA HIS TYR GLY ILE HIS GLY THR ASN ASN PRO ALA SEQRES 11 A 165 SER ILE GLY LYS ALA VAL SER LYS GLY CYS ILE ARG MET SEQRES 12 A 165 HIS ASN LYS ASP VAL ILE GLU LEU ALA SER ILE VAL PRO SEQRES 13 A 165 ASN GLY THR ARG VAL THR ILE ASN ARG SEQRES 1 B 165 GLY MET LEU THR TYR GLN VAL LYS GLN GLY ASP THR LEU SEQRES 2 B 165 ASN SER ILE ALA ALA ASP PHE ARG ILE SER THR ALA ALA SEQRES 3 B 165 LEU LEU GLN ALA ASN PRO SER LEU GLN ALA GLY LEU THR SEQRES 4 B 165 ALA GLY GLN SER ILE VAL ILE PRO GLY LEU PRO ASP PRO SEQRES 5 B 165 TYR THR ILE PRO TYR HIS ILE ALA VAL SER ILE GLY ALA SEQRES 6 B 165 LYS THR LEU THR LEU SER LEU ASN ASN ARG VAL MET LYS SEQRES 7 B 165 THR TYR PRO ILE ALA VAL GLY LYS ILE LEU THR GLN THR SEQRES 8 B 165 PRO THR GLY GLU PHE TYR ILE ILE ASN ARG GLN ARG ASN SEQRES 9 B 165 PRO GLY GLY PRO PHE GLY ALA TYR TRP LEU SER LEU SER SEQRES 10 B 165 ALA ALA HIS TYR GLY ILE HIS GLY THR ASN ASN PRO ALA SEQRES 11 B 165 SER ILE GLY LYS ALA VAL SER LYS GLY CYS ILE ARG MET SEQRES 12 B 165 HIS ASN LYS ASP VAL ILE GLU LEU ALA SER ILE VAL PRO SEQRES 13 B 165 ASN GLY THR ARG VAL THR ILE ASN ARG HET SO4 A1165 5 HET SO4 A1166 5 HET SO4 B1165 5 HET SO4 B1166 5 HET SO4 B1167 5 HET SO4 B1168 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 6(O4 S 2-) FORMUL 9 HOH *166(H2 O) HELIX 1 1 THR A 11 PHE A 19 1 9 HELIX 2 2 SER A 22 ASN A 30 1 9 HELIX 3 3 ASP A 50 ILE A 54 5 5 HELIX 4 4 GLY A 105 GLY A 109 5 5 HELIX 5 5 ASN A 127 ILE A 131 5 5 HELIX 6 6 HIS A 143 VAL A 154 1 12 HELIX 7 7 THR B 11 PHE B 19 1 9 HELIX 8 8 SER B 22 ASN B 30 1 9 HELIX 9 9 PRO B 31 GLY B 36 5 6 HELIX 10 10 ASP B 50 ILE B 54 5 5 HELIX 11 11 GLY B 105 GLY B 109 5 5 HELIX 12 12 ASN B 127 ILE B 131 5 5 HELIX 13 13 HIS B 143 VAL B 154 1 12 SHEET 1 AA 2 LEU A 2 GLN A 5 0 SHEET 2 AA 2 SER A 42 ILE A 45 -1 O ILE A 43 N TYR A 4 SHEET 1 AB 8 ARG A 74 PRO A 80 0 SHEET 2 AB 8 THR A 66 LEU A 71 -1 O LEU A 67 N TYR A 79 SHEET 3 AB 8 TYR A 56 SER A 61 -1 O HIS A 57 N SER A 70 SHEET 4 AB 8 ARG A 159 ASN A 163 1 O ARG A 159 N ILE A 58 SHEET 5 AB 8 GLY A 93 ARG A 102 -1 O GLY A 93 N ILE A 162 SHEET 6 AB 8 TYR A 111 LEU A 115 -1 O TRP A 112 N GLN A 101 SHEET 7 AB 8 GLY A 121 HIS A 123 -1 O ILE A 122 N LEU A 113 SHEET 8 AB 8 ILE A 140 ARG A 141 1 O ILE A 140 N HIS A 123 SHEET 1 AC 2 VAL A 83 GLY A 84 0 SHEET 2 AC 2 ALA A 134 SER A 136 1 N SER A 136 O VAL A 83 SHEET 1 BA 2 LEU B 2 GLN B 5 0 SHEET 2 BA 2 SER B 42 ILE B 45 -1 O ILE B 43 N TYR B 4 SHEET 1 BB 8 ARG B 74 PRO B 80 0 SHEET 2 BB 8 THR B 66 LEU B 71 -1 O LEU B 67 N TYR B 79 SHEET 3 BB 8 TYR B 56 SER B 61 -1 O HIS B 57 N SER B 70 SHEET 4 BB 8 ARG B 159 ASN B 163 1 O ARG B 159 N ILE B 58 SHEET 5 BB 8 GLY B 93 ARG B 102 -1 O GLY B 93 N ILE B 162 SHEET 6 BB 8 TYR B 111 LEU B 115 -1 O TRP B 112 N GLN B 101 SHEET 7 BB 8 GLY B 121 HIS B 123 -1 O ILE B 122 N LEU B 113 SHEET 8 BB 8 ILE B 140 ARG B 141 1 O ILE B 140 N HIS B 123 SHEET 1 BC 2 VAL B 83 GLY B 84 0 SHEET 2 BC 2 ALA B 134 SER B 136 1 N SER B 136 O VAL B 83 SITE 1 AC1 7 HIS A 123 SER A 136 LYS A 137 GLY A 138 SITE 2 AC1 7 CYS A 139 ARG A 141 LYS B 137 SITE 1 AC2 3 ASN A 127 VAL A 135 ARG A 141 SITE 1 AC3 3 THR A 11 ASN A 13 ARG B 102 SITE 1 AC4 7 LYS A 137 HIS B 123 SER B 136 LYS B 137 SITE 2 AC4 7 GLY B 138 CYS B 139 ARG B 141 SITE 1 AC5 6 LYS A 85 LYS A 137 ASN B 127 VAL B 135 SITE 2 AC5 6 ARG B 141 HOH B2070 SITE 1 AC6 2 THR B 11 ASN B 13 CRYST1 56.240 86.280 74.140 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017781 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011590 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013488 0.00000