HEADER HYDROLASE/DNA 16-JUL-15 5CLD TITLE ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING AN TITLE 2 OXOCARBENIUM-INTERMEDIATE ANALOG AND A FREE 3-METHYLADENINE TITLE 3 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*(NRI)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 6 27-SEP-23 5CLD 1 REMARK REVDAT 5 27-NOV-19 5CLD 1 REMARK REVDAT 4 13-SEP-17 5CLD 1 JRNL REMARK REVDAT 3 25-NOV-15 5CLD 1 JRNL REVDAT 2 18-NOV-15 5CLD 1 JRNL REVDAT 1 28-OCT-15 5CLD 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. 1.54 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 44194 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.520 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 34.9875 - 3.7120 0.98 3088 149 0.1356 0.1652 REMARK 3 2 3.7120 - 2.9468 1.00 3105 149 0.1488 0.1688 REMARK 3 3 2.9468 - 2.5744 0.99 3097 143 0.1646 0.2125 REMARK 3 4 2.5744 - 2.3391 0.99 3068 145 0.1564 0.1691 REMARK 3 5 2.3391 - 2.1715 0.98 3059 146 0.1463 0.1847 REMARK 3 6 2.1715 - 2.0435 0.98 3052 149 0.1455 0.1898 REMARK 3 7 2.0435 - 1.9411 0.98 2999 144 0.1591 0.1649 REMARK 3 8 1.9411 - 1.8566 0.98 3023 144 0.1515 0.1750 REMARK 3 9 1.8566 - 1.7852 0.97 3005 136 0.1515 0.1772 REMARK 3 10 1.7852 - 1.7236 0.96 2969 137 0.1467 0.1796 REMARK 3 11 1.7236 - 1.6697 0.96 2943 142 0.1510 0.1856 REMARK 3 12 1.6697 - 1.6220 0.95 2999 139 0.1537 0.2034 REMARK 3 13 1.6220 - 1.5793 0.95 2914 137 0.1510 0.1989 REMARK 3 14 1.5793 - 1.5407 0.93 2876 137 0.1530 0.1793 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2575 REMARK 3 ANGLE : 1.049 3594 REMARK 3 CHIRALITY : 0.043 387 REMARK 3 PLANARITY : 0.006 373 REMARK 3 DIHEDRAL : 18.008 995 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): -6.4559 -21.2075 65.5857 REMARK 3 T TENSOR REMARK 3 T11: 0.1700 T22: 0.1177 REMARK 3 T33: 0.1501 T12: 0.0018 REMARK 3 T13: -0.0255 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 1.2941 L22: 3.8626 REMARK 3 L33: 5.1506 L12: -0.6107 REMARK 3 L13: -0.4066 L23: 3.9058 REMARK 3 S TENSOR REMARK 3 S11: 0.0410 S12: 0.0045 S13: -0.2419 REMARK 3 S21: 0.2056 S22: -0.0058 S23: 0.0201 REMARK 3 S31: 0.4834 S32: -0.0326 S33: -0.0676 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.9740 -7.3364 70.5247 REMARK 3 T TENSOR REMARK 3 T11: 0.0905 T22: 0.1182 REMARK 3 T33: 0.0832 T12: 0.0041 REMARK 3 T13: 0.0109 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 2.6322 L22: 2.1396 REMARK 3 L33: 3.5751 L12: -0.4507 REMARK 3 L13: 1.8453 L23: -0.8704 REMARK 3 S TENSOR REMARK 3 S11: -0.1039 S12: -0.2352 S13: 0.0048 REMARK 3 S21: 0.0987 S22: 0.1189 S23: 0.0882 REMARK 3 S31: -0.0541 S32: -0.2511 S33: -0.0128 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.8944 -12.8514 62.1050 REMARK 3 T TENSOR REMARK 3 T11: 0.1128 T22: 0.1432 REMARK 3 T33: 0.1252 T12: -0.0042 REMARK 3 T13: 0.0070 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 2.5858 L22: 3.0573 REMARK 3 L33: 3.1411 L12: -1.0222 REMARK 3 L13: -0.7367 L23: 1.9027 REMARK 3 S TENSOR REMARK 3 S11: 0.0156 S12: -0.0029 S13: -0.0559 REMARK 3 S21: -0.0235 S22: 0.1331 S23: -0.2914 REMARK 3 S31: 0.0301 S32: 0.3220 S33: -0.1410 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.3942 -20.5189 55.5452 REMARK 3 T TENSOR REMARK 3 T11: 0.1248 T22: 0.0925 REMARK 3 T33: 0.1186 T12: -0.0016 REMARK 3 T13: -0.0148 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 3.0078 L22: 2.6395 REMARK 3 L33: 5.5134 L12: -1.0557 REMARK 3 L13: -2.5364 L23: 1.7411 REMARK 3 S TENSOR REMARK 3 S11: -0.1375 S12: 0.0714 S13: -0.1979 REMARK 3 S21: 0.0379 S22: 0.0467 S23: -0.0497 REMARK 3 S31: 0.4387 S32: -0.0113 S33: 0.1201 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.1728 -11.4881 51.3855 REMARK 3 T TENSOR REMARK 3 T11: 0.1005 T22: 0.0947 REMARK 3 T33: 0.0896 T12: -0.0083 REMARK 3 T13: -0.0067 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.4774 L22: 0.6240 REMARK 3 L33: 1.2378 L12: -0.3077 REMARK 3 L13: -0.1477 L23: 0.0813 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: -0.0025 S13: 0.0241 REMARK 3 S21: -0.0414 S22: 0.0273 S23: -0.0388 REMARK 3 S31: 0.0007 S32: 0.0736 S33: -0.0318 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 119 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.6842 -8.6687 39.0626 REMARK 3 T TENSOR REMARK 3 T11: 0.1011 T22: 0.1065 REMARK 3 T33: 0.0957 T12: -0.0025 REMARK 3 T13: -0.0051 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.9289 L22: 1.2152 REMARK 3 L33: 1.5440 L12: -0.1939 REMARK 3 L13: 0.4224 L23: 0.0693 REMARK 3 S TENSOR REMARK 3 S11: 0.0560 S12: 0.0581 S13: -0.1033 REMARK 3 S21: -0.0632 S22: -0.0116 S23: -0.0343 REMARK 3 S31: -0.0137 S32: 0.0101 S33: -0.0332 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 144 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.3709 -0.2669 43.2166 REMARK 3 T TENSOR REMARK 3 T11: 0.0686 T22: 0.0527 REMARK 3 T33: 0.0643 T12: -0.0033 REMARK 3 T13: -0.0008 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 2.4929 L22: 3.3563 REMARK 3 L33: 3.7998 L12: 0.6621 REMARK 3 L13: -0.7626 L23: -1.4296 REMARK 3 S TENSOR REMARK 3 S11: 0.0585 S12: 0.0065 S13: 0.1527 REMARK 3 S21: -0.0945 S22: -0.0182 S23: -0.1512 REMARK 3 S31: -0.1902 S32: 0.1639 S33: -0.0375 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 178 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.7990 1.6657 41.0634 REMARK 3 T TENSOR REMARK 3 T11: 0.0913 T22: 0.0526 REMARK 3 T33: 0.0612 T12: 0.0149 REMARK 3 T13: -0.0062 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 2.7557 L22: 2.3028 REMARK 3 L33: 2.1451 L12: 0.2495 REMARK 3 L13: 0.1701 L23: -0.1118 REMARK 3 S TENSOR REMARK 3 S11: 0.0818 S12: 0.2051 S13: 0.0863 REMARK 3 S21: -0.2186 S22: 0.0238 S23: 0.0630 REMARK 3 S31: -0.0865 S32: -0.2013 S33: -0.1051 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 179 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.1401 10.0705 44.4827 REMARK 3 T TENSOR REMARK 3 T11: 0.1186 T22: 0.0670 REMARK 3 T33: 0.0796 T12: -0.0074 REMARK 3 T13: 0.0009 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.2243 L22: 1.7330 REMARK 3 L33: 1.1042 L12: 0.2946 REMARK 3 L13: -0.0342 L23: -0.4410 REMARK 3 S TENSOR REMARK 3 S11: -0.0601 S12: 0.0249 S13: 0.1397 REMARK 3 S21: -0.1383 S22: 0.0164 S23: -0.0570 REMARK 3 S31: -0.1057 S32: 0.0299 S33: 0.0411 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 207 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.7975 16.6846 48.0345 REMARK 3 T TENSOR REMARK 3 T11: 0.1636 T22: 0.1163 REMARK 3 T33: 0.1255 T12: -0.0015 REMARK 3 T13: -0.0184 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.9852 L22: 4.1596 REMARK 3 L33: 0.9767 L12: -0.0026 REMARK 3 L13: -0.7029 L23: -0.8324 REMARK 3 S TENSOR REMARK 3 S11: 0.0053 S12: -0.0713 S13: 0.1044 REMARK 3 S21: 0.2647 S22: -0.0054 S23: -0.0516 REMARK 3 S31: -0.1235 S32: -0.0102 S33: 0.0115 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.5596 9.9626 63.3259 REMARK 3 T TENSOR REMARK 3 T11: 0.1741 T22: 0.2242 REMARK 3 T33: 0.2496 T12: 0.0365 REMARK 3 T13: -0.0448 T23: -0.0749 REMARK 3 L TENSOR REMARK 3 L11: 0.2190 L22: 1.9948 REMARK 3 L33: 1.6925 L12: -0.5301 REMARK 3 L13: 0.3890 L23: -0.0988 REMARK 3 S TENSOR REMARK 3 S11: -0.2591 S12: -0.3807 S13: 0.5538 REMARK 3 S21: 0.1917 S22: 0.1440 S23: 0.0555 REMARK 3 S31: -0.1483 S32: 0.1308 S33: -0.0134 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.5445 14.0492 63.7751 REMARK 3 T TENSOR REMARK 3 T11: 0.1684 T22: 0.4726 REMARK 3 T33: 0.5438 T12: 0.0379 REMARK 3 T13: -0.0577 T23: -0.2123 REMARK 3 L TENSOR REMARK 3 L11: 4.2840 L22: 1.4371 REMARK 3 L33: 0.2031 L12: 0.6402 REMARK 3 L13: 0.7861 L23: -0.1620 REMARK 3 S TENSOR REMARK 3 S11: -0.2051 S12: 0.4588 S13: 0.4736 REMARK 3 S21: 0.0751 S22: 0.1454 S23: -0.0271 REMARK 3 S31: -0.0620 S32: -0.1142 S33: -0.0881 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1420 5.5628 60.8196 REMARK 3 T TENSOR REMARK 3 T11: 0.2534 T22: 0.3130 REMARK 3 T33: 0.2749 T12: 0.0824 REMARK 3 T13: 0.0415 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 3.6010 L22: 5.8232 REMARK 3 L33: 0.9486 L12: 1.3395 REMARK 3 L13: 0.8579 L23: -0.4881 REMARK 3 S TENSOR REMARK 3 S11: -0.2810 S12: 0.1665 S13: 0.4952 REMARK 3 S21: -0.5058 S22: 0.2057 S23: -0.7553 REMARK 3 S31: 0.4340 S32: 0.4880 S33: 0.1273 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 5CLD 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_1000211766. 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 : 44235 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.25500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.902 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3BVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% W/V PEG4000, 42 MM SODIUM ACETATE, REMARK 280 PH 4.6, 85 MM AMMONIUM ACETATE, 5% V/V 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 46.41300 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: -11.0 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: 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 B 208 O HOH B 226 2.14 REMARK 500 O HOH A 577 O HOH B 219 2.18 REMARK 500 O HOH A 484 O HOH A 650 2.19 REMARK 500 O HOH A 450 O HOH A 652 2.19 REMARK 500 REMARK 500 REMARK: NULL 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. = 2.6 DEGREES REMARK 500 DG C 23 O4' - C1' - N9 ANGL. DEV. = 2.6 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 54 156.53 70.84 REMARK 500 THR A 118 -73.35 -97.65 REMARK 500 TYR A 134 -46.95 -131.96 REMARK 500 LYS A 158 -122.97 50.63 REMARK 500 REMARK 500 REMARK: NULL 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: 5CLE RELATED DB: PDB DBREF 5CLD A 1 237 UNP R8GWR7 R8GWR7_BACCE 1 237 DBREF 5CLD B 1 12 PDB 5CLD 5CLD 1 12 DBREF 5CLD C 13 24 PDB 5CLD 5CLD 13 24 SEQADV 5CLD GLY A -3 UNP R8GWR7 EXPRESSION TAG SEQADV 5CLD PRO A -2 UNP R8GWR7 EXPRESSION TAG SEQADV 5CLD VAL A -1 UNP R8GWR7 EXPRESSION TAG SEQADV 5CLD 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 NRI DA DG DT DC DC DG SEQRES 1 C 12 DC DG DG DA DC DT DT DT DC DG DG DG HET NRI B 6 11 HET ADK B 101 11 HETNAM NRI PHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL) HETNAM 2 NRI ESTER HETNAM ADK 3-METHYL-3H-PURIN-6-YLAMINE HETSYN ADK 3-METHYLADENINE FORMUL 2 NRI C5 H12 N O5 P FORMUL 4 ADK C6 H7 N5 FORMUL 5 HOH *415(H2 O) HELIX 1 AA1 HIS A 2 ALA A 14 1 13 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 LEU A 71 1 12 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 ALA A 193 1 16 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 NRI B 6 1555 1555 1.60 LINK O3' NRI B 6 P DA B 7 1555 1555 1.60 SITE 1 AC1 8 TYR A 27 DA B 5 NRI B 6 DA B 7 SITE 2 AC1 8 HOH B 206 DT C 18 DT C 19 DT C 20 CRYST1 38.202 92.826 48.309 90.00 113.71 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 0.026177 0.000000 0.011494 0.00000 SCALE2 0.000000 0.010773 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022608 0.00000