HEADER HYDROLASE/DNA 16-JUL-15 5CL6 TITLE ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING A 3- TITLE 2 METHYLADENINE ANALOG OR DNA CONTAINING AN ABASIC SITE AND A FREE TITLE 3 NUCLEOBASE (33% SUBSTRATE/67% PRODUCT AT 72 HOURS) 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*(DZM)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 5CL6 1 REMARK REVDAT 5 27-NOV-19 5CL6 1 REMARK REVDAT 4 13-SEP-17 5CL6 1 JRNL REMARK REVDAT 3 25-NOV-15 5CL6 1 JRNL REVDAT 2 18-NOV-15 5CL6 1 JRNL REVDAT 1 28-OCT-15 5CL6 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) : 35.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 45846 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.380 REMARK 3 FREE R VALUE TEST SET COUNT : 2006 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 35.0570 - 3.7118 0.97 3088 145 0.1379 0.1653 REMARK 3 2 3.7118 - 2.9467 1.00 3159 144 0.1497 0.1885 REMARK 3 3 2.9467 - 2.5743 1.00 3135 145 0.1630 0.1868 REMARK 3 4 2.5743 - 2.3390 1.00 3168 144 0.1628 0.1819 REMARK 3 5 2.3390 - 2.1714 1.00 3139 146 0.1562 0.1842 REMARK 3 6 2.1714 - 2.0434 1.00 3142 140 0.1559 0.1922 REMARK 3 7 2.0434 - 1.9411 1.00 3129 143 0.1668 0.1984 REMARK 3 8 1.9411 - 1.8566 1.00 3147 140 0.1575 0.1788 REMARK 3 9 1.8566 - 1.7851 1.00 3130 143 0.1554 0.1770 REMARK 3 10 1.7851 - 1.7235 1.00 3123 141 0.1485 0.1790 REMARK 3 11 1.7235 - 1.6696 1.00 3111 147 0.1469 0.1870 REMARK 3 12 1.6696 - 1.6219 1.00 3158 139 0.1495 0.1900 REMARK 3 13 1.6219 - 1.5792 1.00 3128 148 0.1626 0.1829 REMARK 3 14 1.5792 - 1.5407 0.99 3083 141 0.1692 0.2106 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) : 18.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.35 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 2647 REMARK 3 ANGLE : 1.043 3709 REMARK 3 CHIRALITY : 0.042 399 REMARK 3 PLANARITY : 0.006 375 REMARK 3 DIHEDRAL : 18.681 1024 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.5248 21.0965 65.7336 REMARK 3 T TENSOR REMARK 3 T11: 0.2274 T22: 0.1392 REMARK 3 T33: 0.1889 T12: -0.0015 REMARK 3 T13: 0.0351 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 1.7354 L22: 5.5781 REMARK 3 L33: 5.7323 L12: -0.5062 REMARK 3 L13: 0.3394 L23: -4.8691 REMARK 3 S TENSOR REMARK 3 S11: 0.0747 S12: -0.0076 S13: 0.3386 REMARK 3 S21: 0.1049 S22: -0.0595 S23: 0.0356 REMARK 3 S31: -0.5252 S32: -0.0367 S33: -0.0363 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.8705 7.0772 70.5474 REMARK 3 T TENSOR REMARK 3 T11: 0.1239 T22: 0.1612 REMARK 3 T33: 0.1297 T12: 0.0013 REMARK 3 T13: -0.0214 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 4.0891 L22: 2.4119 REMARK 3 L33: 5.5541 L12: -0.4912 REMARK 3 L13: -3.6546 L23: 1.1400 REMARK 3 S TENSOR REMARK 3 S11: -0.1251 S12: -0.3185 S13: -0.1031 REMARK 3 S21: 0.0736 S22: 0.0758 S23: -0.1125 REMARK 3 S31: 0.1242 S32: 0.4411 S33: 0.0423 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.8380 12.9144 62.2239 REMARK 3 T TENSOR REMARK 3 T11: 0.1228 T22: 0.1381 REMARK 3 T33: 0.1241 T12: -0.0061 REMARK 3 T13: -0.0176 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 3.8906 L22: 4.9237 REMARK 3 L33: 5.0803 L12: -1.2183 REMARK 3 L13: 0.9344 L23: -2.5589 REMARK 3 S TENSOR REMARK 3 S11: 0.1228 S12: 0.0696 S13: 0.0189 REMARK 3 S21: -0.0241 S22: 0.0751 S23: 0.4632 REMARK 3 S31: -0.1203 S32: -0.3131 S33: -0.1882 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.3995 20.4670 55.6852 REMARK 3 T TENSOR REMARK 3 T11: 0.1751 T22: 0.0996 REMARK 3 T33: 0.1454 T12: -0.0094 REMARK 3 T13: 0.0340 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 4.2005 L22: 3.6511 REMARK 3 L33: 8.3266 L12: -1.3943 REMARK 3 L13: 4.0708 L23: -2.7252 REMARK 3 S TENSOR REMARK 3 S11: -0.1146 S12: 0.1354 S13: 0.2663 REMARK 3 S21: 0.0363 S22: 0.0099 S23: 0.0693 REMARK 3 S31: -0.5330 S32: 0.1226 S33: 0.1330 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.1566 8.1470 46.2773 REMARK 3 T TENSOR REMARK 3 T11: 0.1215 T22: 0.1126 REMARK 3 T33: 0.1198 T12: -0.0241 REMARK 3 T13: -0.0021 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.6234 L22: 0.6381 REMARK 3 L33: 2.2192 L12: -0.4057 REMARK 3 L13: -0.3804 L23: 0.4930 REMARK 3 S TENSOR REMARK 3 S11: 0.0294 S12: 0.0314 S13: -0.0080 REMARK 3 S21: -0.0239 S22: 0.0063 S23: 0.0327 REMARK 3 S31: -0.0554 S32: -0.0919 S33: -0.0365 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): 65.8614 -7.0894 43.3122 REMARK 3 T TENSOR REMARK 3 T11: 0.1237 T22: 0.0857 REMARK 3 T33: 0.0943 T12: -0.0059 REMARK 3 T13: -0.0040 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 1.4444 L22: 2.2539 REMARK 3 L33: 1.1299 L12: 0.4078 REMARK 3 L13: -0.5519 L23: 0.1123 REMARK 3 S TENSOR REMARK 3 S11: -0.0439 S12: 0.0074 S13: -0.1049 REMARK 3 S21: -0.1125 S22: 0.0086 S23: 0.0442 REMARK 3 S31: 0.1681 S32: 0.0027 S33: 0.0304 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 207 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 67.3097 -16.8928 48.0631 REMARK 3 T TENSOR REMARK 3 T11: 0.1875 T22: 0.1527 REMARK 3 T33: 0.1367 T12: 0.0030 REMARK 3 T13: 0.0116 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 1.3711 L22: 6.3131 REMARK 3 L33: 2.2335 L12: 0.7502 REMARK 3 L13: 0.6373 L23: 1.0537 REMARK 3 S TENSOR REMARK 3 S11: 0.0227 S12: -0.1010 S13: -0.0197 REMARK 3 S21: 0.3963 S22: -0.0301 S23: 0.1325 REMARK 3 S31: 0.2793 S32: -0.0438 S33: 0.0227 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 59.9684 -9.6078 62.7889 REMARK 3 T TENSOR REMARK 3 T11: 0.2101 T22: 0.3166 REMARK 3 T33: 0.3062 T12: 0.0385 REMARK 3 T13: 0.0416 T23: 0.0867 REMARK 3 L TENSOR REMARK 3 L11: 0.1443 L22: 2.7697 REMARK 3 L33: 2.1880 L12: -0.4153 REMARK 3 L13: -0.4834 L23: 0.4527 REMARK 3 S TENSOR REMARK 3 S11: -0.2924 S12: -0.6095 S13: -0.6045 REMARK 3 S21: 0.2172 S22: 0.1776 S23: -0.0894 REMARK 3 S31: 0.1307 S32: -0.1588 S33: 0.0278 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 66.0967 -13.9533 64.4962 REMARK 3 T TENSOR REMARK 3 T11: 0.2418 T22: 0.6054 REMARK 3 T33: 0.6076 T12: 0.0806 REMARK 3 T13: 0.0639 T23: 0.2931 REMARK 3 L TENSOR REMARK 3 L11: 6.7416 L22: 2.7407 REMARK 3 L33: 0.2350 L12: -0.5327 REMARK 3 L13: 0.1116 L23: 0.7436 REMARK 3 S TENSOR REMARK 3 S11: -0.2488 S12: 0.2890 S13: -0.6701 REMARK 3 S21: 0.1845 S22: 0.1934 S23: 0.1480 REMARK 3 S31: 0.1169 S32: 0.2490 S33: -0.0979 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.8411 -5.9501 62.2240 REMARK 3 T TENSOR REMARK 3 T11: 0.2300 T22: 0.3606 REMARK 3 T33: 0.2966 T12: 0.1201 REMARK 3 T13: -0.0008 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 6.2096 L22: 8.5524 REMARK 3 L33: 4.4221 L12: 2.4126 REMARK 3 L13: -0.6767 L23: 2.0950 REMARK 3 S TENSOR REMARK 3 S11: -0.3622 S12: -0.3236 S13: -0.6251 REMARK 3 S21: -0.4232 S22: 0.2794 S23: 0.6990 REMARK 3 S31: -0.7669 S32: -0.8366 S33: 0.0447 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 5CL6 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_1000211784. 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 : 45888 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 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 (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.18400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.26 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 (%): 44.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% 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 46.64100 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: 3160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 DC C 17 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG C 23 O4' - C1' - N9 ANGL. DEV. = 2.0 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 54 153.89 73.39 REMARK 500 THR A 118 -71.31 -98.63 REMARK 500 TYR A 134 -44.58 -133.01 REMARK 500 LYS A 158 -121.50 53.30 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 659 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 660 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 661 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 662 DISTANCE = 6.54 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 54K 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: 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 REMARK 900 RELATED ID: 5CLE RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHAIN B CONTAINS MICROHETEROGENEITY AT POSITION 6 (DZM VERSUS ORP). DBREF 5CL6 A 1 237 UNP R8GWR7 R8GWR7_BACCE 1 237 DBREF 5CL6 B 1 12 PDB 5CL6 5CL6 1 12 DBREF 5CL6 C 13 24 PDB 5CL6 5CL6 13 24 SEQADV 5CL6 GLY A -3 UNP R8GWR7 EXPRESSION TAG SEQADV 5CL6 PRO A -2 UNP R8GWR7 EXPRESSION TAG SEQADV 5CL6 VAL A -1 UNP R8GWR7 EXPRESSION TAG SEQADV 5CL6 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 DZM DA DG DT DC DC DG SEQRES 1 C 12 DC DG DG DA DC DT DT DT DC DG DG DG HET DZM B 6 22 HET ORP B 6 12 HET 54K B 101 11 HETNAM DZM 3-DEAZA-3-METHYLADENINE HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM 54K 7-METHYL-3H-IMIDAZO[4,5-C]PYRIDIN-4-AMINE HETSYN DZM 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETSYN 2 DZM PENTOFURANOSYL)-7-METHYL-1H-IMIDAZO[4,5-C]PYRIDIN-4- HETSYN 3 DZM AMINE HETSYN 54K 3-DEAZA-3-METHYLADENINE FORMUL 2 DZM C12 H17 N4 O6 P FORMUL 2 ORP C5 H11 O7 P FORMUL 4 54K C7 H8 N4 FORMUL 5 HOH *413(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 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 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 ADZM B 6 1555 1555 1.61 LINK O3' DA B 5 P BORP B 6 1555 1555 1.61 LINK O3'ADZM B 6 P DA B 7 1555 1555 1.61 LINK O3 BORP B 6 P DA B 7 1555 1555 1.61 SITE 1 AC1 6 TYR A 27 DA B 5 DA B 7 DT C 18 SITE 2 AC1 6 DT C 19 DT C 20 CRYST1 38.389 93.282 48.077 90.00 112.72 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 0.026049 0.000000 0.010908 0.00000 SCALE2 0.000000 0.010720 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022550 0.00000