HEADER TRANSFERASE 15-SEP-11 4A1K TITLE YKUD L,D-TRANSPEPTIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE L, D-TRANSPEPTIDASE YKUD; COMPND 3 CHAIN: A; 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, PEPTIDOGLYCAN SYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR M.BLAISE,S.FUGLSANG MIDTGAARD,S.ROI MIDTGAARD,T.BOESEN,S.THIRUP REVDAT 3 20-DEC-23 4A1K 1 REMARK LINK REVDAT 2 17-JAN-18 4A1K 1 REMARK REVDAT 1 26-SEP-12 4A1K 0 JRNL AUTH M.BLAISE,S.FUGLSANG MIDTGAARD,S.ROI MIDTGAARD,T.BOESEN, JRNL AUTH 2 S.THIRUP JRNL TITL STRUCTURES OF THREE NEW CRYSTAL FORMS OF THE YKUD JRNL TITL 2 L,D-TRANSPEPTIDASE FROM B. SUBTILIS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 22270 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 28.7932 - 4.2138 0.95 1530 152 0.1664 0.1424 REMARK 3 2 4.2138 - 3.3462 1.00 1501 147 0.1553 0.1887 REMARK 3 3 3.3462 - 2.9237 1.00 1480 146 0.1945 0.2331 REMARK 3 4 2.9237 - 2.6566 1.00 1461 144 0.1977 0.2277 REMARK 3 5 2.6566 - 2.4663 1.00 1458 144 0.2028 0.2554 REMARK 3 6 2.4663 - 2.3209 1.00 1431 141 0.1910 0.2379 REMARK 3 7 2.3209 - 2.2048 1.00 1438 142 0.1803 0.2283 REMARK 3 8 2.2048 - 2.1088 1.00 1453 143 0.1770 0.2494 REMARK 3 9 2.1088 - 2.0276 1.00 1414 140 0.1901 0.2262 REMARK 3 10 2.0276 - 1.9577 1.00 1441 141 0.2001 0.2463 REMARK 3 11 1.9577 - 1.8965 1.00 1420 140 0.2149 0.2882 REMARK 3 12 1.8965 - 1.8423 1.00 1415 140 0.2569 0.2750 REMARK 3 13 1.8423 - 1.7938 1.00 1432 141 0.3002 0.3441 REMARK 3 14 1.7938 - 1.7500 1.00 1397 138 0.2891 0.3030 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 52.38 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.520 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.57350 REMARK 3 B22 (A**2) : 8.57350 REMARK 3 B33 (A**2) : 5.12490 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 : 0.007 1299 REMARK 3 ANGLE : 1.052 1775 REMARK 3 CHIRALITY : 0.074 208 REMARK 3 PLANARITY : 0.005 228 REMARK 3 DIHEDRAL : 11.517 476 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 1:12) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3004 20.0887 -17.5526 REMARK 3 T TENSOR REMARK 3 T11: 0.1052 T22: 0.3077 REMARK 3 T33: 0.1132 T12: 0.0508 REMARK 3 T13: 0.0579 T23: 0.0490 REMARK 3 L TENSOR REMARK 3 L11: 3.2862 L22: 1.4395 REMARK 3 L33: 2.8583 L12: -1.2540 REMARK 3 L13: -2.2815 L23: 0.2814 REMARK 3 S TENSOR REMARK 3 S11: 0.0522 S12: 0.3181 S13: 0.0929 REMARK 3 S21: -0.1166 S22: 0.0162 S23: -0.0026 REMARK 3 S31: -0.1404 S32: -0.3199 S33: 0.0096 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 13:29) REMARK 3 ORIGIN FOR THE GROUP (A): 17.0630 23.9562 -8.3766 REMARK 3 T TENSOR REMARK 3 T11: 0.2669 T22: 0.1214 REMARK 3 T33: 0.2170 T12: -0.0363 REMARK 3 T13: 0.1336 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.6542 L22: 5.6994 REMARK 3 L33: 2.2205 L12: 0.5264 REMARK 3 L13: 0.0671 L23: -1.6482 REMARK 3 S TENSOR REMARK 3 S11: 0.3116 S12: -0.0587 S13: 0.4894 REMARK 3 S21: 0.3982 S22: -0.0862 S23: -0.0263 REMARK 3 S31: -0.4480 S32: 0.0972 S33: -0.0033 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 30:42) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6232 29.8352 -18.1509 REMARK 3 T TENSOR REMARK 3 T11: 0.3945 T22: 0.2976 REMARK 3 T33: 0.5607 T12: 0.1600 REMARK 3 T13: 0.1164 T23: 0.1200 REMARK 3 L TENSOR REMARK 3 L11: 3.8087 L22: 1.9624 REMARK 3 L33: 5.5399 L12: 2.6578 REMARK 3 L13: 4.5024 L23: 2.9884 REMARK 3 S TENSOR REMARK 3 S11: -0.3357 S12: -0.2739 S13: 0.8306 REMARK 3 S21: -0.4308 S22: -0.0784 S23: 0.5912 REMARK 3 S31: -1.0654 S32: -0.7026 S33: 0.4500 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 43:56) REMARK 3 ORIGIN FOR THE GROUP (A): 26.5678 16.0329 -15.3478 REMARK 3 T TENSOR REMARK 3 T11: 0.1315 T22: 0.1708 REMARK 3 T33: 0.1149 T12: -0.0136 REMARK 3 T13: 0.0506 T23: 0.0233 REMARK 3 L TENSOR REMARK 3 L11: 2.0832 L22: 4.9163 REMARK 3 L33: 0.3123 L12: -2.5286 REMARK 3 L13: 0.0112 L23: -0.7738 REMARK 3 S TENSOR REMARK 3 S11: 0.2309 S12: 0.2695 S13: 0.2001 REMARK 3 S21: -0.0700 S22: -0.2029 S23: -0.0715 REMARK 3 S31: -0.1320 S32: -0.0697 S33: -0.0285 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 57:66) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6524 -1.0578 -15.3025 REMARK 3 T TENSOR REMARK 3 T11: 0.2605 T22: 0.1729 REMARK 3 T33: 0.1032 T12: -0.0303 REMARK 3 T13: -0.0260 T23: -0.0354 REMARK 3 L TENSOR REMARK 3 L11: 4.4924 L22: 3.3483 REMARK 3 L33: 1.9587 L12: 2.6594 REMARK 3 L13: 1.1766 L23: 0.5025 REMARK 3 S TENSOR REMARK 3 S11: -0.3412 S12: 0.4511 S13: 0.1138 REMARK 3 S21: -0.5926 S22: 0.1306 S23: 0.1904 REMARK 3 S31: 0.0420 S32: -0.0339 S33: 0.1741 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 67:81) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0585 -4.9702 -15.5959 REMARK 3 T TENSOR REMARK 3 T11: 0.2025 T22: 0.1031 REMARK 3 T33: 0.1518 T12: -0.0323 REMARK 3 T13: 0.0753 T23: -0.0727 REMARK 3 L TENSOR REMARK 3 L11: 4.8282 L22: 2.8741 REMARK 3 L33: 1.8229 L12: 0.8187 REMARK 3 L13: -0.5179 L23: 0.2171 REMARK 3 S TENSOR REMARK 3 S11: -0.0452 S12: 0.3969 S13: -0.0946 REMARK 3 S21: -0.5309 S22: 0.1060 S23: -0.4048 REMARK 3 S31: -0.0671 S32: 0.1987 S33: -0.0791 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 82:93) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7006 2.6929 -9.8141 REMARK 3 T TENSOR REMARK 3 T11: 0.1631 T22: 0.1419 REMARK 3 T33: 0.1736 T12: -0.0777 REMARK 3 T13: -0.0785 T23: 0.0477 REMARK 3 L TENSOR REMARK 3 L11: 5.0231 L22: 0.3082 REMARK 3 L33: 0.6927 L12: -0.6445 REMARK 3 L13: 1.2857 L23: 0.1212 REMARK 3 S TENSOR REMARK 3 S11: -0.0188 S12: -0.0931 S13: 0.0390 REMARK 3 S21: -0.1199 S22: 0.0564 S23: 0.1966 REMARK 3 S31: 0.0439 S32: -0.0933 S33: -0.0222 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 94:103) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9362 8.8189 -7.3758 REMARK 3 T TENSOR REMARK 3 T11: 0.0773 T22: 0.0983 REMARK 3 T33: 0.0692 T12: -0.0156 REMARK 3 T13: 0.0240 T23: 0.0219 REMARK 3 L TENSOR REMARK 3 L11: 2.1898 L22: 2.4828 REMARK 3 L33: 5.2984 L12: 0.7794 REMARK 3 L13: 0.5047 L23: -1.3876 REMARK 3 S TENSOR REMARK 3 S11: 0.0278 S12: 0.0654 S13: -0.0570 REMARK 3 S21: -0.0904 S22: -0.0897 S23: -0.1339 REMARK 3 S31: 0.1279 S32: 0.2642 S33: 0.0487 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 104:144) REMARK 3 ORIGIN FOR THE GROUP (A): 12.9805 1.6082 -2.0196 REMARK 3 T TENSOR REMARK 3 T11: 0.1168 T22: 0.1159 REMARK 3 T33: 0.1353 T12: -0.0343 REMARK 3 T13: -0.0333 T23: 0.0557 REMARK 3 L TENSOR REMARK 3 L11: 0.3842 L22: 0.6525 REMARK 3 L33: 1.2801 L12: -0.1007 REMARK 3 L13: -0.6273 L23: -0.2348 REMARK 3 S TENSOR REMARK 3 S11: 0.0434 S12: -0.1550 S13: -0.2560 REMARK 3 S21: -0.0709 S22: 0.0383 S23: 0.2004 REMARK 3 S31: 0.1765 S32: -0.0784 S33: -0.0401 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 145:154) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0273 -3.8413 -3.6817 REMARK 3 T TENSOR REMARK 3 T11: 0.1762 T22: 0.0879 REMARK 3 T33: 0.1506 T12: 0.0083 REMARK 3 T13: -0.0077 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 4.9713 L22: 4.2672 REMARK 3 L33: 6.0651 L12: 0.4146 REMARK 3 L13: -0.8989 L23: -2.7068 REMARK 3 S TENSOR REMARK 3 S11: -0.0103 S12: 0.0206 S13: -0.8067 REMARK 3 S21: -0.0933 S22: -0.1548 S23: -0.2512 REMARK 3 S31: 0.5885 S32: 0.0121 S33: 0.1335 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 155:165) REMARK 3 ORIGIN FOR THE GROUP (A): 19.2285 5.2137 -14.6441 REMARK 3 T TENSOR REMARK 3 T11: 0.1494 T22: 0.0673 REMARK 3 T33: 0.0593 T12: -0.0118 REMARK 3 T13: 0.0252 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 7.3633 L22: 4.7292 REMARK 3 L33: 5.6838 L12: 0.8857 REMARK 3 L13: 0.7081 L23: -0.6733 REMARK 3 S TENSOR REMARK 3 S11: 0.0082 S12: 0.3246 S13: 0.1385 REMARK 3 S21: -0.3548 S22: -0.1470 S23: 0.2318 REMARK 3 S31: 0.0994 S32: -0.0734 S33: 0.1435 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 4A1K 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_1290049674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-11 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 : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH SX-165 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22287 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 53.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 15.96 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 15.01 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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 (%): 58.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS PH 6.5, 3 M NACL AND REMARK 280 2MM MURNAC MONOSACCHARIDE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 58.87500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.95000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.43750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.95000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.31250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.95000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.95000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.43750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.95000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.95000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 88.31250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.87500 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: 1940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2027 LIES ON A SPECIAL POSITION. 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 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 2127 O HOH A 2128 1.87 REMARK 500 OH CME A 139 O HOH A 2186 2.03 REMARK 500 O HOH A 2046 O HOH A 2099 2.09 REMARK 500 O HOH A 2014 O HOH A 2025 2.11 REMARK 500 NE ARG A 141 O2 SO4 A 1165 2.12 REMARK 500 O HOH A 2104 O HOH A 2210 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 137 O1 SO4 A 1165 7555 1.92 REMARK 500 O HOH A 2004 O HOH A 2025 6554 2.09 REMARK 500 O HOH A 2036 O HOH A 2162 7555 2.18 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 GLN A 34 -8.49 -55.49 REMARK 500 ASN A 73 -2.30 76.82 REMARK 500 MET A 76 -61.43 -96.04 REMARK 500 SER A 116 40.78 -75.84 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 A2063 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A2094 DISTANCE = 6.10 ANGSTROMS 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 A 1165 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 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: 4A1J RELATED DB: PDB REMARK 900 YKUD L,D-TRANSPEPTIDASE FROM B.SUBTILIS 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 DBREF 4A1K A 1 164 UNP O34816 YKUD_BACSU 1 164 SEQADV 4A1K GLY A 0 UNP O34816 EXPRESSION TAG SEQADV 4A1K ALA A 117 UNP O34816 LYS 117 ENGINEERED MUTATION SEQADV 4A1K ALA A 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 CME 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 MODRES 4A1K CME A 139 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET CME A 139 10 HET SO4 A1165 5 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM SO4 SULFATE ION FORMUL 1 CME C5 H11 N O3 S2 FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *211(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 PRO A 31 GLY A 36 5 6 HELIX 4 4 ASP A 50 ILE A 54 5 5 HELIX 5 5 ILE A 86 GLN A 89 5 4 HELIX 6 6 GLY A 105 GLY A 109 5 5 HELIX 7 7 ASN A 127 ILE A 131 5 5 HELIX 8 8 HIS A 143 VAL A 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 LINK C GLY A 138 N CME A 139 1555 1555 1.34 LINK C CME A 139 N AILE A 140 1555 1555 1.33 LINK C CME A 139 N BILE A 140 1555 1555 1.33 SITE 1 AC1 6 SER A 136 LYS A 137 GLY A 138 CME A 139 SITE 2 AC1 6 ARG A 141 HOH A2188 CRYST1 59.900 59.900 117.750 90.00 90.00 90.00 P 41 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 0.016694 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008493 0.00000