HEADER HYDROLASE/DNA 16-JUL-15 5CL4 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 (71% SUBSTRATE/29% PRODUCT AT 24 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 5CL4 1 REMARK REVDAT 5 27-NOV-19 5CL4 1 REMARK REVDAT 4 06-SEP-17 5CL4 1 JRNL REMARK REVDAT 3 25-NOV-15 5CL4 1 JRNL REVDAT 2 18-NOV-15 5CL4 1 JRNL REVDAT 1 28-OCT-15 5CL4 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. 1.87 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 25801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1296 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 35.2811 - 3.8800 1.00 2771 146 0.1294 0.1586 REMARK 3 2 3.8800 - 3.0802 1.00 2745 147 0.1452 0.1790 REMARK 3 3 3.0802 - 2.6910 1.00 2704 146 0.1624 0.2043 REMARK 3 4 2.6910 - 2.4451 1.00 2750 143 0.1710 0.2408 REMARK 3 5 2.4451 - 2.2698 1.00 2724 144 0.1599 0.2213 REMARK 3 6 2.2698 - 2.1360 1.00 2726 144 0.1560 0.1938 REMARK 3 7 2.1360 - 2.0291 1.00 2714 144 0.1681 0.2376 REMARK 3 8 2.0291 - 1.9407 1.00 2721 141 0.1954 0.2561 REMARK 3 9 1.9407 - 1.8660 0.97 2650 141 0.2156 0.2665 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.20 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 2630 REMARK 3 ANGLE : 1.021 3682 REMARK 3 CHIRALITY : 0.042 396 REMARK 3 PLANARITY : 0.006 371 REMARK 3 DIHEDRAL : 19.364 1011 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.4801 20.9622 65.5998 REMARK 3 T TENSOR REMARK 3 T11: 0.3744 T22: 0.2233 REMARK 3 T33: 0.2955 T12: -0.0137 REMARK 3 T13: 0.0258 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 2.9213 L22: 9.4049 REMARK 3 L33: 7.3294 L12: -2.1779 REMARK 3 L13: 1.2626 L23: -7.2660 REMARK 3 S TENSOR REMARK 3 S11: -0.0586 S12: 0.0154 S13: 0.5099 REMARK 3 S21: 0.3764 S22: -0.1337 S23: -0.0839 REMARK 3 S31: -0.7797 S32: -0.0258 S33: 0.1454 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.6470 6.8108 70.4394 REMARK 3 T TENSOR REMARK 3 T11: 0.2217 T22: 0.2140 REMARK 3 T33: 0.1563 T12: 0.0123 REMARK 3 T13: -0.0306 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 6.2971 L22: 2.6189 REMARK 3 L33: 6.5442 L12: -0.5066 REMARK 3 L13: -5.5591 L23: 1.7819 REMARK 3 S TENSOR REMARK 3 S11: -0.1215 S12: -0.5396 S13: -0.1503 REMARK 3 S21: 0.2218 S22: 0.0547 S23: -0.0663 REMARK 3 S31: 0.1045 S32: 0.4082 S33: 0.0792 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.6726 12.7854 62.1048 REMARK 3 T TENSOR REMARK 3 T11: 0.2571 T22: 0.2538 REMARK 3 T33: 0.2538 T12: -0.0151 REMARK 3 T13: -0.0221 T23: -0.0261 REMARK 3 L TENSOR REMARK 3 L11: 5.6003 L22: 3.8290 REMARK 3 L33: 7.7555 L12: -2.7599 REMARK 3 L13: 2.7488 L23: -5.3113 REMARK 3 S TENSOR REMARK 3 S11: 0.1618 S12: -0.0874 S13: -0.0501 REMARK 3 S21: -0.0121 S22: 0.2587 S23: 0.5208 REMARK 3 S31: -0.0931 S32: -0.3538 S33: -0.4060 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.3420 20.3211 55.6022 REMARK 3 T TENSOR REMARK 3 T11: 0.2829 T22: 0.2028 REMARK 3 T33: 0.1960 T12: -0.0015 REMARK 3 T13: 0.0415 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 4.5373 L22: 6.5958 REMARK 3 L33: 9.8626 L12: -4.3054 REMARK 3 L13: 6.6181 L23: -5.7916 REMARK 3 S TENSOR REMARK 3 S11: -0.2027 S12: -0.0231 S13: 0.2682 REMARK 3 S21: 0.1991 S22: 0.0270 S23: -0.1364 REMARK 3 S31: -0.7912 S32: 0.0939 S33: 0.3278 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.1145 10.2388 47.0210 REMARK 3 T TENSOR REMARK 3 T11: 0.1955 T22: 0.1506 REMARK 3 T33: 0.1568 T12: -0.0242 REMARK 3 T13: 0.0075 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.4040 L22: 1.0147 REMARK 3 L33: 3.8283 L12: -0.4278 REMARK 3 L13: -0.6766 L23: 0.3911 REMARK 3 S TENSOR REMARK 3 S11: 0.0149 S12: 0.0011 S13: -0.0077 REMARK 3 S21: -0.0491 S22: -0.0087 S23: 0.0307 REMARK 3 S31: -0.0462 S32: -0.1037 S33: -0.0010 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 144 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.7897 0.0031 43.1597 REMARK 3 T TENSOR REMARK 3 T11: 0.1950 T22: 0.1457 REMARK 3 T33: 0.1421 T12: -0.0029 REMARK 3 T13: 0.0011 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 6.6081 L22: 6.5272 REMARK 3 L33: 8.7585 L12: 2.7176 REMARK 3 L13: 3.4355 L23: 3.6094 REMARK 3 S TENSOR REMARK 3 S11: -0.0114 S12: 0.1492 S13: -0.1606 REMARK 3 S21: -0.2779 S22: 0.0785 S23: 0.2748 REMARK 3 S31: 0.1106 S32: -0.1424 S33: -0.0929 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 178 ) REMARK 3 ORIGIN FOR THE GROUP (A): 69.0219 -2.3125 40.3711 REMARK 3 T TENSOR REMARK 3 T11: 0.2072 T22: 0.1854 REMARK 3 T33: 0.1520 T12: 0.0160 REMARK 3 T13: 0.0266 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 2.2193 L22: 4.8581 REMARK 3 L33: 8.8920 L12: -0.2232 REMARK 3 L13: 3.7576 L23: -1.5127 REMARK 3 S TENSOR REMARK 3 S11: 0.1608 S12: 0.0584 S13: -0.1641 REMARK 3 S21: -0.3695 S22: -0.0555 S23: 0.0575 REMARK 3 S31: 0.1466 S32: 0.2437 S33: -0.1770 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 179 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 64.8909 -13.3018 45.9596 REMARK 3 T TENSOR REMARK 3 T11: 0.2558 T22: 0.1785 REMARK 3 T33: 0.1890 T12: -0.0197 REMARK 3 T13: 0.0270 T23: 0.0154 REMARK 3 L TENSOR REMARK 3 L11: 1.5283 L22: 5.2211 REMARK 3 L33: 1.7333 L12: -0.1866 REMARK 3 L13: -0.0314 L23: 1.5511 REMARK 3 S TENSOR REMARK 3 S11: -0.0291 S12: -0.0266 S13: -0.2702 REMARK 3 S21: 0.0014 S22: -0.0266 S23: 0.0628 REMARK 3 S31: 0.2820 S32: -0.0096 S33: 0.0668 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 59.5946 -9.9539 62.6733 REMARK 3 T TENSOR REMARK 3 T11: 0.2429 T22: 0.3859 REMARK 3 T33: 0.4087 T12: 0.0658 REMARK 3 T13: 0.0434 T23: 0.1074 REMARK 3 L TENSOR REMARK 3 L11: 0.1110 L22: 3.3383 REMARK 3 L33: 3.0310 L12: -0.6130 REMARK 3 L13: -0.1485 L23: 0.6480 REMARK 3 S TENSOR REMARK 3 S11: -0.3529 S12: -0.7994 S13: -0.9684 REMARK 3 S21: 0.2083 S22: 0.3030 S23: -0.0757 REMARK 3 S31: 0.1000 S32: -0.1280 S33: -0.0804 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 65.6443 -14.1653 64.2306 REMARK 3 T TENSOR REMARK 3 T11: 0.2058 T22: 0.6247 REMARK 3 T33: 0.7013 T12: 0.0416 REMARK 3 T13: 0.0861 T23: 0.2759 REMARK 3 L TENSOR REMARK 3 L11: 5.1937 L22: 3.8432 REMARK 3 L33: 0.2938 L12: -2.0118 REMARK 3 L13: -0.8878 L23: 1.0005 REMARK 3 S TENSOR REMARK 3 S11: -0.5358 S12: 0.1450 S13: -0.8566 REMARK 3 S21: 0.3782 S22: 0.3769 S23: 0.4549 REMARK 3 S31: 0.2129 S32: 0.1560 S33: -0.1434 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.5771 -6.0020 62.0490 REMARK 3 T TENSOR REMARK 3 T11: 0.2854 T22: 0.4360 REMARK 3 T33: 0.3529 T12: 0.0844 REMARK 3 T13: 0.0068 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 6.6912 L22: 8.8121 REMARK 3 L33: 5.0028 L12: 2.0391 REMARK 3 L13: -1.2287 L23: 0.2239 REMARK 3 S TENSOR REMARK 3 S11: -0.5530 S12: -0.4443 S13: -0.7664 REMARK 3 S21: -0.3154 S22: 0.7242 S23: 0.8213 REMARK 3 S31: -0.8681 S32: -1.1085 S33: 0.0713 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 5CL4 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_1000211728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-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 : 25843 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.866 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 : 5.300 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.216 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 (%): 46.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 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 46.77900 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: 3110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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. = 2.1 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 54 158.98 63.69 REMARK 500 THR A 118 -72.93 -93.67 REMARK 500 TYR A 134 -46.34 -132.82 REMARK 500 LYS A 158 -119.74 51.83 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 54K B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CL3 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 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 5CL4 A 1 237 UNP R8GWR7 R8GWR7_BACCE 1 237 DBREF 5CL4 B 1 12 PDB 5CL4 5CL4 1 12 DBREF 5CL4 C 13 24 PDB 5CL4 5CL4 13 24 SEQADV 5CL4 GLY A -3 UNP R8GWR7 EXPRESSION TAG SEQADV 5CL4 PRO A -2 UNP R8GWR7 EXPRESSION TAG SEQADV 5CL4 VAL A -1 UNP R8GWR7 EXPRESSION TAG SEQADV 5CL4 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 *207(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 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 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 38.247 93.558 47.976 90.00 112.74 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 0.026146 0.000000 0.010957 0.00000 SCALE2 0.000000 0.010689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022600 0.00000