HEADER HYDROLASE/DNA 16-JUL-15 5CLE TITLE ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING AN ABASIC- TITLE 2 SITE ANALOG AND A FREE 3-METHYLADENINE NUCLEOBASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKD; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*CP*GP*AP*(3DR)P*AP*GP*TP*CP*CP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3'); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 ATCC: 14579; SOURCE 5 GENE: IKE_03968; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HMS174; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBG103; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS DNA GLYCOSYLASE, HEAT-LIKE REPEAT, PROTEIN-DNA COMPLEX, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.A.MULLINS,B.F.EICHMAN REVDAT 7 27-SEP-23 5CLE 1 REMARK REVDAT 6 27-NOV-19 5CLE 1 REMARK REVDAT 5 22-NOV-17 5CLE 1 REMARK REVDAT 4 13-SEP-17 5CLE 1 JRNL REMARK REVDAT 3 25-NOV-15 5CLE 1 JRNL REVDAT 2 18-NOV-15 5CLE 1 JRNL REVDAT 1 28-OCT-15 5CLE 0 JRNL AUTH E.A.MULLINS,R.SHI,Z.D.PARSONS,P.K.YUEN,S.S.DAVID,Y.IGARASHI, JRNL AUTH 2 B.F.EICHMAN JRNL TITL THE DNA GLYCOSYLASE ALKD USES A NON-BASE-FLIPPING MECHANISM JRNL TITL 2 TO EXCISE BULKY LESIONS. JRNL REF NATURE V. 527 254 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26524531 JRNL DOI 10.1038/NATURE15728 REMARK 2 REMARK 2 RESOLUTION. 1.73 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 32539 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1626 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 40.0898 - 3.9604 0.99 2624 139 0.1266 0.1477 REMARK 3 2 3.9604 - 3.1439 1.00 2593 136 0.1436 0.1569 REMARK 3 3 3.1439 - 2.7466 1.00 2583 134 0.1611 0.2088 REMARK 3 4 2.7466 - 2.4955 1.00 2607 137 0.1694 0.2126 REMARK 3 5 2.4955 - 2.3167 1.00 2571 138 0.1557 0.1967 REMARK 3 6 2.3167 - 2.1801 1.00 2587 135 0.1537 0.2163 REMARK 3 7 2.1801 - 2.0709 1.00 2567 131 0.1539 0.1959 REMARK 3 8 2.0709 - 1.9808 1.00 2568 132 0.1710 0.2313 REMARK 3 9 1.9808 - 1.9045 1.00 2579 140 0.1765 0.2367 REMARK 3 10 1.9045 - 1.8388 1.00 2567 133 0.1831 0.2223 REMARK 3 11 1.8388 - 1.7813 1.00 2581 137 0.2006 0.2585 REMARK 3 12 1.7813 - 1.7304 0.96 2486 134 0.2106 0.2880 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.10 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 : 0.007 2562 REMARK 3 ANGLE : 1.009 3574 REMARK 3 CHIRALITY : 0.044 385 REMARK 3 PLANARITY : 0.006 370 REMARK 3 DIHEDRAL : 17.902 984 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.6169 22.3933 21.3777 REMARK 3 T TENSOR REMARK 3 T11: 0.2514 T22: 0.1574 REMARK 3 T33: 0.1975 T12: -0.0177 REMARK 3 T13: 0.0349 T23: -0.0168 REMARK 3 L TENSOR REMARK 3 L11: 2.1510 L22: 8.8667 REMARK 3 L33: 6.3370 L12: -1.8926 REMARK 3 L13: 1.3153 L23: -7.2674 REMARK 3 S TENSOR REMARK 3 S11: 0.0715 S12: 0.0826 S13: 0.2657 REMARK 3 S21: 0.3007 S22: -0.0445 S23: 0.0418 REMARK 3 S31: -0.6027 S32: 0.0721 S33: -0.0280 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1505 8.4712 26.3169 REMARK 3 T TENSOR REMARK 3 T11: 0.1062 T22: 0.1233 REMARK 3 T33: 0.0967 T12: -0.0005 REMARK 3 T13: -0.0207 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 5.5003 L22: 3.9219 REMARK 3 L33: 6.5879 L12: -1.1159 REMARK 3 L13: -3.5136 L23: 1.9213 REMARK 3 S TENSOR REMARK 3 S11: -0.1506 S12: -0.3555 S13: -0.0807 REMARK 3 S21: 0.1711 S22: 0.1612 S23: -0.1408 REMARK 3 S31: 0.0450 S32: 0.3909 S33: 0.0077 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 53 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4492 12.2779 19.8400 REMARK 3 T TENSOR REMARK 3 T11: 0.1338 T22: 0.1817 REMARK 3 T33: 0.1360 T12: -0.0283 REMARK 3 T13: -0.0029 T23: -0.0106 REMARK 3 L TENSOR REMARK 3 L11: 7.2452 L22: 7.5999 REMARK 3 L33: 7.3365 L12: -4.5411 REMARK 3 L13: 4.4185 L23: -5.3498 REMARK 3 S TENSOR REMARK 3 S11: 0.0577 S12: -0.2276 S13: -0.2688 REMARK 3 S21: -0.0563 S22: 0.2546 S23: 0.6295 REMARK 3 S31: 0.0862 S32: -0.4828 S33: -0.2105 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 54 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.3511 21.7077 11.0292 REMARK 3 T TENSOR REMARK 3 T11: 0.1952 T22: 0.0803 REMARK 3 T33: 0.1478 T12: 0.0110 REMARK 3 T13: 0.0235 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 6.2580 L22: 3.3689 REMARK 3 L33: 6.2200 L12: -1.0423 REMARK 3 L13: 2.1166 L23: -2.4102 REMARK 3 S TENSOR REMARK 3 S11: -0.0721 S12: 0.2973 S13: 0.2666 REMARK 3 S21: 0.0764 S22: 0.0108 S23: 0.1782 REMARK 3 S31: -0.3797 S32: 0.0462 S33: 0.0893 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5746 13.2336 10.4112 REMARK 3 T TENSOR REMARK 3 T11: 0.1304 T22: 0.1713 REMARK 3 T33: 0.1171 T12: -0.0018 REMARK 3 T13: 0.0119 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 8.0102 L22: 2.1891 REMARK 3 L33: 3.2890 L12: -0.0428 REMARK 3 L13: 4.8822 L23: 0.0004 REMARK 3 S TENSOR REMARK 3 S11: 0.0695 S12: 0.4008 S13: -0.2272 REMARK 3 S21: -0.0668 S22: 0.0621 S23: 0.1235 REMARK 3 S31: 0.0677 S32: 0.0604 S33: -0.1365 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 103 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.6371 16.4345 -0.0645 REMARK 3 T TENSOR REMARK 3 T11: 0.1620 T22: 0.1225 REMARK 3 T33: 0.1072 T12: -0.0040 REMARK 3 T13: 0.0296 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 3.6651 L22: 7.0316 REMARK 3 L33: 6.9780 L12: -4.2842 REMARK 3 L13: 4.5872 L23: -5.0776 REMARK 3 S TENSOR REMARK 3 S11: -0.1060 S12: -0.1541 S13: 0.0736 REMARK 3 S21: -0.2678 S22: -0.0147 S23: -0.1505 REMARK 3 S31: -0.1520 S32: -0.2244 S33: 0.1125 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 104 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.4803 9.3688 0.3308 REMARK 3 T TENSOR REMARK 3 T11: 0.1340 T22: 0.0728 REMARK 3 T33: 0.1330 T12: -0.0011 REMARK 3 T13: 0.0125 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 1.1203 L22: 1.1170 REMARK 3 L33: 6.5969 L12: -0.2164 REMARK 3 L13: 0.2095 L23: -0.0918 REMARK 3 S TENSOR REMARK 3 S11: 0.0395 S12: 0.0250 S13: 0.0099 REMARK 3 S21: -0.0251 S22: 0.0356 S23: 0.0428 REMARK 3 S31: 0.1294 S32: -0.0911 S33: -0.0727 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 144 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.4137 1.4366 -1.0052 REMARK 3 T TENSOR REMARK 3 T11: 0.1323 T22: 0.0881 REMARK 3 T33: 0.0900 T12: -0.0039 REMARK 3 T13: 0.0137 T23: 0.0219 REMARK 3 L TENSOR REMARK 3 L11: 4.2833 L22: 6.5633 REMARK 3 L33: 6.7113 L12: 2.3588 REMARK 3 L13: 2.9455 L23: 3.5789 REMARK 3 S TENSOR REMARK 3 S11: 0.0773 S12: -0.0406 S13: -0.1858 REMARK 3 S21: -0.1546 S22: -0.0016 S23: 0.1744 REMARK 3 S31: 0.2585 S32: -0.1953 S33: -0.0663 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 178 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.7545 -0.7302 -3.8031 REMARK 3 T TENSOR REMARK 3 T11: 0.1537 T22: 0.0547 REMARK 3 T33: 0.1021 T12: 0.0197 REMARK 3 T13: 0.0159 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 7.9517 L22: 5.5463 REMARK 3 L33: 5.6764 L12: 0.8851 REMARK 3 L13: 0.7239 L23: 0.5817 REMARK 3 S TENSOR REMARK 3 S11: 0.0862 S12: 0.3153 S13: -0.2567 REMARK 3 S21: -0.2803 S22: 0.0912 S23: -0.1394 REMARK 3 S31: 0.2213 S32: 0.1881 S33: -0.1397 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 179 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.7209 -11.8217 1.7491 REMARK 3 T TENSOR REMARK 3 T11: 0.1958 T22: 0.1053 REMARK 3 T33: 0.1101 T12: -0.0064 REMARK 3 T13: 0.0159 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 1.1060 L22: 5.8003 REMARK 3 L33: 0.9252 L12: -0.2686 REMARK 3 L13: -0.2555 L23: 1.2349 REMARK 3 S TENSOR REMARK 3 S11: -0.0915 S12: 0.0072 S13: -0.1776 REMARK 3 S21: 0.1373 S22: 0.0388 S23: 0.0408 REMARK 3 S31: 0.2065 S32: 0.0262 S33: 0.0371 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.6423 -8.5881 19.2477 REMARK 3 T TENSOR REMARK 3 T11: 0.1803 T22: 0.2757 REMARK 3 T33: 0.2993 T12: 0.0798 REMARK 3 T13: 0.0690 T23: 0.0859 REMARK 3 L TENSOR REMARK 3 L11: 0.1056 L22: 3.1149 REMARK 3 L33: 3.1346 L12: -0.5186 REMARK 3 L13: -0.2286 L23: 0.5442 REMARK 3 S TENSOR REMARK 3 S11: -0.4698 S12: -0.5077 S13: -0.6657 REMARK 3 S21: 0.0812 S22: 0.2749 S23: -0.1744 REMARK 3 S31: 0.0718 S32: -0.1328 S33: -0.0999 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.8200 -12.6566 19.7879 REMARK 3 T TENSOR REMARK 3 T11: 0.1409 T22: 0.6461 REMARK 3 T33: 0.5925 T12: 0.0853 REMARK 3 T13: 0.0861 T23: 0.2703 REMARK 3 L TENSOR REMARK 3 L11: 5.9961 L22: 3.7173 REMARK 3 L33: 1.4150 L12: -4.1210 REMARK 3 L13: -2.4122 L23: 2.2682 REMARK 3 S TENSOR REMARK 3 S11: -0.4478 S12: 0.4183 S13: -0.7879 REMARK 3 S21: 0.2742 S22: 0.0347 S23: 0.1438 REMARK 3 S31: 0.4525 S32: 0.7419 S33: 0.0265 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.3551 -4.0799 16.7056 REMARK 3 T TENSOR REMARK 3 T11: 0.2913 T22: 0.4393 REMARK 3 T33: 0.3798 T12: 0.0897 REMARK 3 T13: -0.0280 T23: -0.0438 REMARK 3 L TENSOR REMARK 3 L11: 3.3757 L22: 2.9547 REMARK 3 L33: 3.2097 L12: 2.9142 REMARK 3 L13: 2.2422 L23: 1.2020 REMARK 3 S TENSOR REMARK 3 S11: -0.3375 S12: 0.0307 S13: -0.6451 REMARK 3 S21: -0.2497 S22: 0.3648 S23: 0.8565 REMARK 3 S31: -0.7848 S32: -0.9509 S33: 0.1551 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 5CLE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32574 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.44300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.383 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 3BVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% W/V PEG4000, 42 MM SODIUM ACETATE, REMARK 280 PH 4.6, 85 MM AMMONIUM ACETATE, 5% GLYCEROL, PH 5.7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 46.64400 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 -3 REMARK 465 PRO A -2 REMARK 465 GLU A 230 REMARK 465 LYS A 231 REMARK 465 ILE A 232 REMARK 465 GLY A 233 REMARK 465 GLU A 234 REMARK 465 THR A 235 REMARK 465 LEU A 236 REMARK 465 SER A 237 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG C 14 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC C 17 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES 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 THR A 54 156.19 66.55 REMARK 500 THR A 118 -71.89 -91.72 REMARK 500 TYR A 134 -44.67 -131.23 REMARK 500 LYS A 158 -122.22 53.36 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 A 567 DISTANCE = 6.22 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADK B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CL3 RELATED DB: PDB REMARK 900 RELATED ID: 5CL4 RELATED DB: PDB REMARK 900 RELATED ID: 5CL5 RELATED DB: PDB REMARK 900 RELATED ID: 5CL6 RELATED DB: PDB REMARK 900 RELATED ID: 5CL7 RELATED DB: PDB REMARK 900 RELATED ID: 5CL8 RELATED DB: PDB REMARK 900 RELATED ID: 5CL9 RELATED DB: PDB REMARK 900 RELATED ID: 5CLA RELATED DB: PDB REMARK 900 RELATED ID: 5CLB RELATED DB: PDB REMARK 900 RELATED ID: 5CLC RELATED DB: PDB REMARK 900 RELATED ID: 5CLD RELATED DB: PDB DBREF 5CLE A 1 237 UNP R8GWR7 R8GWR7_BACCE 1 237 DBREF 5CLE B 1 12 PDB 5CLE 5CLE 1 12 DBREF 5CLE C 13 24 PDB 5CLE 5CLE 13 24 SEQADV 5CLE GLY A -3 UNP R8GWR7 EXPRESSION TAG SEQADV 5CLE PRO A -2 UNP R8GWR7 EXPRESSION TAG SEQADV 5CLE VAL A -1 UNP R8GWR7 EXPRESSION TAG SEQADV 5CLE PRO A 0 UNP R8GWR7 EXPRESSION TAG SEQRES 1 A 241 GLY PRO VAL PRO MET HIS PRO PHE VAL LYS ALA LEU GLN SEQRES 2 A 241 GLU HIS PHE THR ALA HIS GLN ASN PRO GLU LYS ALA GLU SEQRES 3 A 241 PRO MET ALA ARG TYR MET LYS ASN HIS PHE LEU PHE LEU SEQRES 4 A 241 GLY ILE GLN THR PRO GLU ARG ARG GLN LEU LEU LYS ASP SEQRES 5 A 241 ILE ILE GLN ILE HIS THR LEU PRO ASP GLN LYS ASP PHE SEQRES 6 A 241 GLN ILE ILE ILE ARG GLU LEU TRP ASP LEU PRO GLU ARG SEQRES 7 A 241 GLU PHE GLN ALA ALA ALA LEU ASP ILE MET GLN LYS TYR SEQRES 8 A 241 LYS LYS HIS ILE ASN GLU THR HIS ILE PRO PHE LEU GLU SEQRES 9 A 241 GLU LEU ILE VAL THR LYS SER TRP TRP ASP SER VAL ASP SEQRES 10 A 241 SER ILE VAL PRO THR PHE LEU GLY ASP ILE PHE LEU LYS SEQRES 11 A 241 HIS PRO GLU LEU ILE SER ALA TYR ILE PRO LYS TRP ILE SEQRES 12 A 241 ALA SER ASP ASN ILE TRP LEU GLN ARG ALA ALA ILE LEU SEQRES 13 A 241 PHE GLN LEU LYS TYR LYS GLN LYS MET ASP GLU GLU LEU SEQRES 14 A 241 LEU PHE TRP ILE ILE GLY GLN LEU HIS SER SER LYS GLU SEQRES 15 A 241 PHE PHE ILE GLN LYS ALA ILE GLY TRP VAL LEU ARG GLU SEQRES 16 A 241 TYR ALA LYS THR ASN PRO ASP VAL VAL TRP GLU TYR VAL SEQRES 17 A 241 GLN ASN ASN GLU LEU ALA PRO LEU SER LYS ARG GLU ALA SEQRES 18 A 241 ILE LYS HIS ILE LYS GLN ASN TYR GLY ILE ASN ASN GLU SEQRES 19 A 241 LYS ILE GLY GLU THR LEU SER SEQRES 1 B 12 DC DC DC DG DA 3DR DA DG DT DC DC DG SEQRES 1 C 12 DC DG DG DA DC DT DT DT DC DG DG DG HET 3DR B 6 11 HET ADK B 101 11 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM ADK 3-METHYL-3H-PURIN-6-YLAMINE HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN ADK 3-METHYLADENINE FORMUL 2 3DR C5 H11 O6 P FORMUL 4 ADK C6 H7 N5 FORMUL 5 HOH *328(H2 O) HELIX 1 AA1 HIS A 2 HIS A 15 1 14 HELIX 2 AA2 ASN A 17 MET A 28 1 12 HELIX 3 AA3 GLN A 38 THR A 54 1 17 HELIX 4 AA4 ASP A 57 LYS A 59 5 3 HELIX 5 AA5 ASP A 60 ASP A 70 1 11 HELIX 6 AA6 GLU A 73 TYR A 87 1 15 HELIX 7 AA7 LYS A 88 ILE A 91 5 4 HELIX 8 AA8 ASN A 92 THR A 94 5 3 HELIX 9 AA9 HIS A 95 VAL A 104 1 10 HELIX 10 AB1 TRP A 108 VAL A 116 1 9 HELIX 11 AB2 THR A 118 HIS A 127 1 10 HELIX 12 AB3 PRO A 128 ALA A 133 5 6 HELIX 13 AB4 TYR A 134 SER A 141 1 8 HELIX 14 AB5 ASN A 143 PHE A 153 1 11 HELIX 15 AB6 TYR A 157 MET A 161 5 5 HELIX 16 AB7 ASP A 162 HIS A 174 1 13 HELIX 17 AB8 GLU A 178 LYS A 194 1 17 HELIX 18 AB9 ASN A 196 ASN A 207 1 12 HELIX 19 AC1 ALA A 210 ILE A 218 1 9 HELIX 20 AC2 ILE A 221 GLY A 226 1 6 LINK O3' DA B 5 P 3DR B 6 1555 1555 1.61 LINK O3' 3DR B 6 P DA B 7 1555 1555 1.61 SITE 1 AC1 8 TYR A 27 DA B 5 3DR B 6 DA B 7 SITE 2 AC1 8 HOH B 211 DT C 18 DT C 19 DT C 20 CRYST1 38.492 93.288 48.162 90.00 112.84 90.00 P 1 21 1 2 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 0.025979 0.000000 0.010945 0.00000 SCALE2 0.000000 0.010719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022531 0.00000