HEADER LIGASE 16-MAY-19 6P0A TITLE HUMAN DNA LIGASE 1 BOUND TO AN ADENYLATED, DIDEOXY TERMINATED DNA NICK TITLE 2 WITH 2 MM MG2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 262-904; COMPND 5 SYNONYM: DNA LIGASE I,POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP] 1; COMPND 6 EC: 6.5.1.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'- COMPND 18 D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LIG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG7; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, PHOSPHOTRANSFERASE, OB FOLD, DNA BINDING DOMAIN, KEYWDS 2 ADENYLATION DOMAIN, METALLOENZYME, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHELLENBERG,R.S.WILLIAMS,P.S.TUMBALE,A.A.RICCIO REVDAT 2 11-OCT-23 6P0A 1 LINK REVDAT 1 11-DEC-19 6P0A 0 JRNL AUTH P.P.TUMBALE,T.J.JURKIW,M.J.SCHELLENBERG,A.A.RICCIO, JRNL AUTH 2 P.J.O'BRIEN,R.S.WILLIAMS JRNL TITL TWO-TIERED ENFORCEMENT OF HIGH-FIDELITY DNA LIGATION. JRNL REF NAT COMMUN V. 10 5431 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31780661 JRNL DOI 10.1038/S41467-019-13478-7 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 50592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2563 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 41.5180 - 5.3547 0.97 2845 151 0.1663 0.1602 REMARK 3 2 5.3547 - 4.2515 0.99 2761 150 0.1276 0.1744 REMARK 3 3 4.2515 - 3.7145 1.00 2732 168 0.1339 0.1682 REMARK 3 4 3.7145 - 3.3751 0.99 2730 154 0.1451 0.1783 REMARK 3 5 3.3751 - 3.1332 0.96 2618 128 0.1678 0.1983 REMARK 3 6 3.1332 - 2.9486 0.98 2674 151 0.1756 0.2271 REMARK 3 7 2.9486 - 2.8009 0.99 2698 128 0.1850 0.2324 REMARK 3 8 2.8009 - 2.6790 0.99 2701 133 0.1762 0.2315 REMARK 3 9 2.6790 - 2.5759 1.00 2656 171 0.1856 0.2122 REMARK 3 10 2.5759 - 2.4870 1.00 2711 141 0.1791 0.1881 REMARK 3 11 2.4870 - 2.4093 1.00 2676 144 0.1916 0.2399 REMARK 3 12 2.4093 - 2.3404 1.00 2720 123 0.1934 0.2312 REMARK 3 13 2.3404 - 2.2788 0.99 2679 145 0.1999 0.2572 REMARK 3 14 2.2788 - 2.2232 0.96 2559 131 0.2255 0.2792 REMARK 3 15 2.2232 - 2.1727 0.96 2588 137 0.2336 0.2730 REMARK 3 16 2.1727 - 2.1264 0.97 2629 132 0.2459 0.3159 REMARK 3 17 2.1264 - 2.0839 0.97 2566 139 0.2600 0.2908 REMARK 3 18 2.0839 - 2.0446 0.92 2486 137 0.2783 0.3557 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 6011 REMARK 3 ANGLE : 0.663 8306 REMARK 3 CHIRALITY : 0.042 932 REMARK 3 PLANARITY : 0.004 954 REMARK 3 DIHEDRAL : 19.099 3570 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 260 THROUGH 455 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0570 -3.8077 45.2103 REMARK 3 T TENSOR REMARK 3 T11: 0.2279 T22: 0.2897 REMARK 3 T33: 0.2261 T12: -0.0182 REMARK 3 T13: -0.0056 T23: -0.0279 REMARK 3 L TENSOR REMARK 3 L11: 1.1156 L22: 2.4515 REMARK 3 L33: 1.5719 L12: 0.4963 REMARK 3 L13: -0.1736 L23: -0.8031 REMARK 3 S TENSOR REMARK 3 S11: 0.0384 S12: -0.1146 S13: 0.0623 REMARK 3 S21: -0.0288 S22: -0.0915 S23: -0.1894 REMARK 3 S31: -0.1283 S32: 0.2427 S33: 0.0636 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 456 THROUGH 544 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.1619 -19.5356 54.8662 REMARK 3 T TENSOR REMARK 3 T11: 0.2422 T22: 0.2558 REMARK 3 T33: 0.2278 T12: -0.0239 REMARK 3 T13: 0.0402 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 2.6920 L22: 1.6881 REMARK 3 L33: 3.7365 L12: -1.2394 REMARK 3 L13: 2.5393 L23: -1.7657 REMARK 3 S TENSOR REMARK 3 S11: 0.0044 S12: -0.2220 S13: -0.0604 REMARK 3 S21: 0.0581 S22: -0.0189 S23: 0.0436 REMARK 3 S31: 0.0601 S32: -0.0852 S33: 0.0027 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 545 THROUGH 741 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.1098 -18.3070 29.3663 REMARK 3 T TENSOR REMARK 3 T11: 0.2267 T22: 0.3167 REMARK 3 T33: 0.3045 T12: -0.0138 REMARK 3 T13: -0.0063 T23: 0.0388 REMARK 3 L TENSOR REMARK 3 L11: 1.3943 L22: 1.8787 REMARK 3 L33: 1.8265 L12: -0.2725 REMARK 3 L13: -0.2375 L23: 0.1298 REMARK 3 S TENSOR REMARK 3 S11: -0.0122 S12: 0.0984 S13: -0.0587 REMARK 3 S21: -0.0220 S22: 0.0091 S23: 0.1398 REMARK 3 S31: 0.0226 S32: -0.1386 S33: 0.0031 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 742 THROUGH 784 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2242 -18.0130 15.5824 REMARK 3 T TENSOR REMARK 3 T11: 0.2222 T22: 0.1711 REMARK 3 T33: 0.2311 T12: 0.0651 REMARK 3 T13: -0.0091 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 2.9909 L22: 1.7010 REMARK 3 L33: 5.1221 L12: 2.1554 REMARK 3 L13: -3.2875 L23: -1.9006 REMARK 3 S TENSOR REMARK 3 S11: -0.2444 S12: 0.4145 S13: -0.1467 REMARK 3 S21: -0.2100 S22: 0.2841 S23: 0.0542 REMARK 3 S31: 0.2242 S32: -0.2733 S33: -0.0614 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 785 THROUGH 901 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.7315 -13.2012 7.7254 REMARK 3 T TENSOR REMARK 3 T11: 0.2869 T22: 0.2818 REMARK 3 T33: 0.1855 T12: -0.0620 REMARK 3 T13: 0.0280 T23: -0.0204 REMARK 3 L TENSOR REMARK 3 L11: 3.6776 L22: 2.4437 REMARK 3 L33: 3.8014 L12: -0.0196 REMARK 3 L13: -0.3589 L23: -0.8099 REMARK 3 S TENSOR REMARK 3 S11: -0.0216 S12: 0.3758 S13: 0.0339 REMARK 3 S21: -0.2403 S22: 0.0436 S23: 0.0479 REMARK 3 S31: 0.0487 S32: -0.0349 S33: -0.0014 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.6619 4.9235 22.9069 REMARK 3 T TENSOR REMARK 3 T11: 0.3750 T22: 0.2515 REMARK 3 T33: 0.2902 T12: -0.0045 REMARK 3 T13: -0.0153 T23: -0.0398 REMARK 3 L TENSOR REMARK 3 L11: 2.0424 L22: 8.1034 REMARK 3 L33: 0.2712 L12: 1.7918 REMARK 3 L13: -0.0030 L23: -0.9441 REMARK 3 S TENSOR REMARK 3 S11: -0.0527 S12: -0.0962 S13: 0.1970 REMARK 3 S21: -0.5292 S22: -0.2078 S23: -0.1134 REMARK 3 S31: -0.1287 S32: -0.0621 S33: 0.2748 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8803 -23.5691 28.3412 REMARK 3 T TENSOR REMARK 3 T11: 0.2638 T22: 0.1897 REMARK 3 T33: 0.2989 T12: -0.0276 REMARK 3 T13: 0.0576 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 2.0377 L22: 3.3728 REMARK 3 L33: 4.5748 L12: -0.6865 REMARK 3 L13: 2.3399 L23: -1.8026 REMARK 3 S TENSOR REMARK 3 S11: 0.0612 S12: 0.0091 S13: -0.0248 REMARK 3 S21: -0.1257 S22: 0.0069 S23: 0.1625 REMARK 3 S31: 0.3434 S32: -0.0377 S33: -0.1100 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 9 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9703 -20.9453 32.9530 REMARK 3 T TENSOR REMARK 3 T11: 0.1745 T22: 0.1987 REMARK 3 T33: 0.2819 T12: 0.0242 REMARK 3 T13: -0.0105 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 2.8218 L22: 5.6895 REMARK 3 L33: 7.1305 L12: 3.1481 REMARK 3 L13: -2.9369 L23: -4.2210 REMARK 3 S TENSOR REMARK 3 S11: 0.0644 S12: 0.2678 S13: 0.1903 REMARK 3 S21: -0.0529 S22: 0.3519 S23: 0.5480 REMARK 3 S31: -0.1304 S32: -0.1299 S33: -0.3964 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 16 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.1629 4.5182 22.6002 REMARK 3 T TENSOR REMARK 3 T11: 0.3130 T22: 0.2810 REMARK 3 T33: 0.2773 T12: -0.0354 REMARK 3 T13: -0.0020 T23: 0.0411 REMARK 3 L TENSOR REMARK 3 L11: 0.0986 L22: 6.9160 REMARK 3 L33: 0.6536 L12: -0.3923 REMARK 3 L13: -0.2536 L23: 0.7680 REMARK 3 S TENSOR REMARK 3 S11: -0.0680 S12: 0.0666 S13: 0.1803 REMARK 3 S21: 0.1859 S22: 0.0535 S23: -0.0952 REMARK 3 S31: -0.0605 S32: 0.1527 S33: 0.0309 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 6P0A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241660. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50667 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 1.33100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1X9N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 100 MM LITHIUM ACETATE, 15 REMARK 280 % (W/V) PEG 3350, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 31.32200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.76900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.42350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.76900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.32200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.42350 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 ARG A 387 REMARK 465 SER A 388 REMARK 465 THR A 389 REMARK 465 GLN A 902 REMARK 465 ILE A 903 REMARK 465 GLN A 904 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DC B 13 O3' 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 HE ARG A 683 O HOH A 1110 1.56 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 DC D 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT D 22 O4' - C1' - N1 ANGL. DEV. = 2.2 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 HIS A 436 -123.86 50.51 REMARK 500 ALA A 455 -147.77 -134.59 REMARK 500 GLU A 692 -55.73 -139.63 REMARK 500 SER A 718 35.94 75.30 REMARK 500 ASP A 728 -35.61 -130.21 REMARK 500 ARG A 738 114.26 -164.96 REMARK 500 HIS A 740 68.04 -103.57 REMARK 500 ASP A 827 -109.59 47.18 REMARK 500 SER A 839 -46.02 -157.39 REMARK 500 ILE A 854 -35.85 -130.91 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 A1612 DISTANCE = 6.00 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 592 OE1 REMARK 620 2 HOH A1208 O 163.9 REMARK 620 3 HOH A1327 O 87.1 83.9 REMARK 620 4 HOH A1340 O 85.4 80.2 81.9 REMARK 620 5 DG B 11 OP1 105.8 88.1 93.7 167.9 REMARK 620 6 HOH B 132 O 99.2 88.5 171.1 92.2 90.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP C 101 DBREF 6P0A A 262 904 UNP P18858 DNLI1_HUMAN 262 904 DBREF 6P0A B 3 13 PDB 6P0A 6P0A 3 13 DBREF 6P0A C 1 7 PDB 6P0A 6P0A 1 7 DBREF 6P0A D 9 26 PDB 6P0A 6P0A 9 26 SEQADV 6P0A SER A 260 UNP P18858 EXPRESSION TAG SEQADV 6P0A ASN A 261 UNP P18858 EXPRESSION TAG SEQRES 1 A 645 SER ASN ASP PRO SER GLY TYR ASN PRO ALA LYS ASN ASN SEQRES 2 A 645 TYR HIS PRO VAL GLU ASP ALA CYS TRP LYS PRO GLY GLN SEQRES 3 A 645 LYS VAL PRO TYR LEU ALA VAL ALA ARG THR PHE GLU LYS SEQRES 4 A 645 ILE GLU GLU VAL SER ALA ARG LEU ARG MET VAL GLU THR SEQRES 5 A 645 LEU SER ASN LEU LEU ARG SER VAL VAL ALA LEU SER PRO SEQRES 6 A 645 PRO ASP LEU LEU PRO VAL LEU TYR LEU SER LEU ASN HIS SEQRES 7 A 645 LEU GLY PRO PRO GLN GLN GLY LEU GLU LEU GLY VAL GLY SEQRES 8 A 645 ASP GLY VAL LEU LEU LYS ALA VAL ALA GLN ALA THR GLY SEQRES 9 A 645 ARG GLN LEU GLU SER VAL ARG ALA GLU ALA ALA GLU LYS SEQRES 10 A 645 GLY ASP VAL GLY LEU VAL ALA GLU ASN SER ARG SER THR SEQRES 11 A 645 GLN ARG LEU MET LEU PRO PRO PRO PRO LEU THR ALA SER SEQRES 12 A 645 GLY VAL PHE SER LYS PHE ARG ASP ILE ALA ARG LEU THR SEQRES 13 A 645 GLY SER ALA SER THR ALA LYS LYS ILE ASP ILE ILE LYS SEQRES 14 A 645 GLY LEU PHE VAL ALA CYS ARG HIS SER GLU ALA ARG PHE SEQRES 15 A 645 ILE ALA ARG SER LEU SER GLY ARG LEU ARG LEU GLY LEU SEQRES 16 A 645 ALA GLU GLN SER VAL LEU ALA ALA LEU SER GLN ALA VAL SEQRES 17 A 645 SER LEU THR PRO PRO GLY GLN GLU PHE PRO PRO ALA MET SEQRES 18 A 645 VAL ASP ALA GLY LYS GLY LYS THR ALA GLU ALA ARG LYS SEQRES 19 A 645 THR TRP LEU GLU GLU GLN GLY MET ILE LEU LYS GLN THR SEQRES 20 A 645 PHE CYS GLU VAL PRO ASP LEU ASP ARG ILE ILE PRO VAL SEQRES 21 A 645 LEU LEU GLU HIS GLY LEU GLU ARG LEU PRO GLU HIS CYS SEQRES 22 A 645 LYS LEU SER PRO GLY ILE PRO LEU LYS PRO MET LEU ALA SEQRES 23 A 645 HIS PRO THR ARG GLY ILE SER GLU VAL LEU LYS ARG PHE SEQRES 24 A 645 GLU GLU ALA ALA PHE THR CYS GLU TYR LYS TYR ASP GLY SEQRES 25 A 645 GLN ARG ALA GLN ILE HIS ALA LEU GLU GLY GLY GLU VAL SEQRES 26 A 645 LYS ILE PHE SER ARG ASN GLN GLU ASP ASN THR GLY LYS SEQRES 27 A 645 TYR PRO ASP ILE ILE SER ARG ILE PRO LYS ILE LYS LEU SEQRES 28 A 645 PRO SER VAL THR SER PHE ILE LEU ASP THR GLU ALA VAL SEQRES 29 A 645 ALA TRP ASP ARG GLU LYS LYS GLN ILE GLN PRO PHE GLN SEQRES 30 A 645 VAL LEU THR THR ARG LYS ARG LYS GLU VAL ASP ALA SER SEQRES 31 A 645 GLU ILE GLN VAL GLN VAL CYS LEU TYR ALA PHE ASP LEU SEQRES 32 A 645 ILE TYR LEU ASN GLY GLU SER LEU VAL ARG GLU PRO LEU SEQRES 33 A 645 SER ARG ARG ARG GLN LEU LEU ARG GLU ASN PHE VAL GLU SEQRES 34 A 645 THR GLU GLY GLU PHE VAL PHE ALA THR SER LEU ASP THR SEQRES 35 A 645 LYS ASP ILE GLU GLN ILE ALA GLU PHE LEU GLU GLN SER SEQRES 36 A 645 VAL LYS ASP SER CYS GLU GLY LEU MET VAL LYS THR LEU SEQRES 37 A 645 ASP VAL ASP ALA THR TYR GLU ILE ALA LYS ARG SER HIS SEQRES 38 A 645 ASN TRP LEU LYS LEU LYS LYS ASP TYR LEU ASP GLY VAL SEQRES 39 A 645 GLY ASP THR LEU ASP LEU VAL VAL ILE GLY ALA TYR LEU SEQRES 40 A 645 GLY ARG GLY LYS ARG ALA GLY ARG TYR GLY GLY PHE LEU SEQRES 41 A 645 LEU ALA SER TYR ASP GLU ASP SER GLU GLU LEU GLN ALA SEQRES 42 A 645 ILE CYS LYS LEU GLY THR GLY PHE SER ASP GLU GLU LEU SEQRES 43 A 645 GLU GLU HIS HIS GLN SER LEU LYS ALA LEU VAL LEU PRO SEQRES 44 A 645 SER PRO ARG PRO TYR VAL ARG ILE ASP GLY ALA VAL ILE SEQRES 45 A 645 PRO ASP HIS TRP LEU ASP PRO SER ALA VAL TRP GLU VAL SEQRES 46 A 645 LYS CYS ALA ASP LEU SER LEU SER PRO ILE TYR PRO ALA SEQRES 47 A 645 ALA ARG GLY LEU VAL ASP SER ASP LYS GLY ILE SER LEU SEQRES 48 A 645 ARG PHE PRO ARG PHE ILE ARG VAL ARG GLU ASP LYS GLN SEQRES 49 A 645 PRO GLU GLN ALA THR THR SER ALA GLN VAL ALA CYS LEU SEQRES 50 A 645 TYR ARG LYS GLN SER GLN ILE GLN SEQRES 1 B 11 DG DC DT DG DA DT DG DC DG DT DC SEQRES 1 C 7 DG DT DC DG DG DA DC SEQRES 1 D 18 DG DT DC DC DG DA DC DG DA DC DG DC DA SEQRES 2 D 18 DT DC DA DG DC HET MG A1001 1 HET AMP C 101 29 HETNAM MG MAGNESIUM ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 5 MG MG 2+ FORMUL 6 AMP C10 H14 N5 O7 P FORMUL 7 HOH *663(H2 O) HELIX 1 AA1 ASP A 262 TYR A 266 5 5 HELIX 2 AA2 PRO A 288 GLU A 301 1 14 HELIX 3 AA3 ALA A 304 SER A 323 1 20 HELIX 4 AA4 ASP A 326 ASN A 336 1 11 HELIX 5 AA5 PRO A 340 GLY A 344 5 5 HELIX 6 AA6 GLY A 350 GLY A 363 1 14 HELIX 7 AA7 GLN A 365 GLY A 377 1 13 HELIX 8 AA8 ASP A 378 ASN A 385 1 8 HELIX 9 AA9 THR A 400 LEU A 414 1 15 HELIX 10 AB1 ALA A 418 CYS A 434 1 17 HELIX 11 AB2 SER A 437 SER A 447 1 11 HELIX 12 AB3 ALA A 455 THR A 470 1 16 HELIX 13 AB4 THR A 488 VAL A 510 1 23 HELIX 14 AB5 ASP A 512 GLY A 524 1 13 HELIX 15 AB6 ARG A 527 CYS A 532 1 6 HELIX 16 AB7 GLY A 550 PHE A 558 1 9 HELIX 17 AB8 ASN A 594 LYS A 597 5 4 HELIX 18 AB9 TYR A 598 LYS A 609 1 12 HELIX 19 AC1 PRO A 634 THR A 639 1 6 HELIX 20 AC2 ASP A 647 ILE A 651 5 5 HELIX 21 AC3 PRO A 674 PHE A 686 1 13 HELIX 22 AC4 ASP A 703 ASP A 717 1 15 HELIX 23 AC5 LYS A 746 LEU A 750 5 5 HELIX 24 AC6 ARG A 768 ALA A 772 5 5 HELIX 25 AC7 SER A 801 ALA A 814 1 14 HELIX 26 AC8 GLN A 883 ALA A 887 5 5 HELIX 27 AC9 THR A 889 GLN A 900 1 12 SHEET 1 AA1 5 ALA A 545 PRO A 547 0 SHEET 2 AA1 5 TRP A 742 LEU A 745 1 O TRP A 742 N HIS A 546 SHEET 3 AA1 5 GLY A 721 THR A 726 -1 N VAL A 724 O LEU A 743 SHEET 4 AA1 5 PHE A 563 LYS A 568 -1 N GLU A 566 O MET A 723 SHEET 5 AA1 5 SER A 698 ASP A 700 -1 O LEU A 699 N CYS A 565 SHEET 1 AA2 5 VAL A 584 PHE A 587 0 SHEET 2 AA2 5 GLN A 572 ALA A 578 -1 N HIS A 577 O LYS A 585 SHEET 3 AA2 5 PHE A 616 ASP A 626 -1 O ALA A 622 N GLN A 572 SHEET 4 AA2 5 VAL A 655 LEU A 665 -1 O CYS A 656 N VAL A 623 SHEET 5 AA2 5 GLU A 668 SER A 669 -1 O GLU A 668 N LEU A 665 SHEET 1 AA3 4 GLN A 631 ILE A 632 0 SHEET 2 AA3 4 PHE A 616 ASP A 626 -1 N ASP A 626 O GLN A 631 SHEET 3 AA3 4 VAL A 655 LEU A 665 -1 O CYS A 656 N VAL A 623 SHEET 4 AA3 4 PHE A 693 PHE A 695 1 O VAL A 694 N LEU A 657 SHEET 1 AA4 6 VAL A 816 LEU A 817 0 SHEET 2 AA4 6 HIS A 834 LEU A 836 -1 O TRP A 835 N LEU A 817 SHEET 3 AA4 6 ASP A 755 LEU A 766 -1 N ALA A 764 O HIS A 834 SHEET 4 AA4 6 TYR A 775 ASP A 784 -1 O GLY A 777 N TYR A 765 SHEET 5 AA4 6 GLU A 789 LEU A 796 -1 O GLU A 789 N ASP A 784 SHEET 6 AA4 6 VAL A 824 ARG A 825 1 O ARG A 825 N LEU A 790 SHEET 1 AA5 5 VAL A 816 LEU A 817 0 SHEET 2 AA5 5 HIS A 834 LEU A 836 -1 O TRP A 835 N LEU A 817 SHEET 3 AA5 5 ASP A 755 LEU A 766 -1 N ALA A 764 O HIS A 834 SHEET 4 AA5 5 VAL A 841 CYS A 846 -1 O VAL A 844 N LEU A 757 SHEET 5 AA5 5 ARG A 874 VAL A 878 -1 O ARG A 877 N GLU A 843 SHEET 1 AA6 2 ASP A 848 SER A 852 0 SHEET 2 AA6 2 GLY A 867 ARG A 871 -1 O ARG A 871 N ASP A 848 LINK P DG C 1 O3P AMP C 101 1555 1555 1.59 LINK OE1 GLU A 592 MG MG A1001 1555 1555 2.08 LINK MG MG A1001 O HOH A1208 1555 1555 2.13 LINK MG MG A1001 O HOH A1327 1555 1555 1.99 LINK MG MG A1001 O HOH A1340 1555 1555 2.07 LINK MG MG A1001 OP1 DG B 11 1555 1555 1.90 LINK MG MG A1001 O HOH B 132 1555 1555 2.18 CISPEP 1 PHE A 476 PRO A 477 0 -1.25 SITE 1 AC1 6 GLU A 592 HOH A1208 HOH A1327 HOH A1340 SITE 2 AC1 6 DG B 11 HOH B 132 SITE 1 AC2 15 GLU A 566 TYR A 567 LYS A 568 TYR A 569 SITE 2 AC2 15 ARG A 573 ARG A 589 GLU A 621 PHE A 660 SITE 3 AC2 15 MET A 723 LYS A 725 LYS A 744 DG C 1 SITE 4 AC2 15 HOH C 208 HOH C 215 HOH C 219 CRYST1 62.644 110.847 115.538 90.00 90.00 90.00 P 21 21 21 4 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 0.015963 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009021 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008655 0.00000