HEADER TRANSFERASE 10-MAR-21 7M09 TITLE PRE-CATALYTIC QUATERNARY COMPLEX OF DNA POLYMERASE LAMBDA WITH BLUNT- TITLE 2 ENDED DSB SUBSTRATE AND INCOMING DUMPNPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 5 KAPPA; COMPND 6 EC: 2.7.7.7,4.2.99.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*A)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*GP*C)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 5; COMPND 21 MOLECULE: DNA (5'-D(*GP*CP*AP*CP*TP*G)-3'); COMPND 22 CHAIN: U; COMPND 23 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: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEXM; 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; SOURCE 22 MOL_ID: 5; SOURCE 23 SYNTHETIC: YES; SOURCE 24 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 25 ORGANISM_TAXID: 32630 KEYWDS NONHOMOLOGOUS END-JOINING, BASE EXCISION REPAIR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.KAMINSKI,K.BEBENEK,L.C.PEDERSEN,T.A.KUNKEL REVDAT 3 25-OCT-23 7M09 1 REMARK REVDAT 2 15-FEB-23 7M09 1 JRNL REVDAT 1 16-MAR-22 7M09 0 JRNL AUTH A.M.KAMINSKI,K.K.CHIRUVELLA,D.A.RAMSDEN,K.BEBENEK, JRNL AUTH 2 T.A.KUNKEL,L.C.PEDERSEN JRNL TITL ANALYSIS OF DIVERSE DOUBLE-STRAND BREAK SYNAPSIS WITH POL JRNL TITL 2 LAMBDA REVEALS BASIS FOR UNIQUE SUBSTRATE SPECIFICITY IN JRNL TITL 3 NONHOMOLOGOUS END-JOINING. JRNL REF NAT COMMUN V. 13 3806 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35778389 JRNL DOI 10.1038/S41467-022-31278-4 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 57346 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2870 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 39.1700 - 4.5400 1.00 2801 145 0.1728 0.1606 REMARK 3 2 4.5400 - 3.6000 1.00 2696 141 0.1388 0.1490 REMARK 3 3 3.6000 - 3.1500 1.00 2629 140 0.1489 0.1816 REMARK 3 4 3.1500 - 2.8600 1.00 2643 142 0.1688 0.1839 REMARK 3 5 2.8600 - 2.6600 0.99 2606 126 0.1665 0.1748 REMARK 3 6 2.6600 - 2.5000 1.00 2600 146 0.1617 0.1859 REMARK 3 7 2.5000 - 2.3700 1.00 2601 129 0.1656 0.1853 REMARK 3 8 2.3700 - 2.2700 1.00 2586 138 0.1649 0.1917 REMARK 3 9 2.2700 - 2.1800 1.00 2597 139 0.1688 0.1991 REMARK 3 10 2.1800 - 2.1100 1.00 2595 131 0.1727 0.2013 REMARK 3 11 2.1100 - 2.0400 1.00 2572 147 0.1695 0.2019 REMARK 3 12 2.0400 - 1.9800 1.00 2580 128 0.1630 0.1904 REMARK 3 13 1.9800 - 1.9300 1.00 2563 134 0.1652 0.1781 REMARK 3 14 1.9300 - 1.8800 1.00 2581 141 0.1725 0.1858 REMARK 3 15 1.8800 - 1.8400 1.00 2580 141 0.1857 0.2532 REMARK 3 16 1.8400 - 1.8000 1.00 2546 136 0.2035 0.2588 REMARK 3 17 1.8000 - 1.7700 1.00 2589 130 0.2488 0.2929 REMARK 3 18 1.7700 - 1.7300 1.00 2562 117 0.2004 0.2160 REMARK 3 19 1.7300 - 1.7000 1.00 2519 163 0.2054 0.2214 REMARK 3 20 1.7000 - 1.6700 1.00 2614 120 0.2137 0.2491 REMARK 3 21 1.6700 - 1.6500 0.95 2416 136 0.2470 0.2674 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) : 0.177 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.819 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.41 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 : 0.010 3195 REMARK 3 ANGLE : 1.035 4430 REMARK 3 CHIRALITY : 0.061 491 REMARK 3 PLANARITY : 0.008 500 REMARK 3 DIHEDRAL : 12.303 984 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 238:329 REMARK 3 ORIGIN FOR THE GROUP (A): -7.7959 25.6396 -25.9119 REMARK 3 T TENSOR REMARK 3 T11: 0.2880 T22: 0.3083 REMARK 3 T33: 0.2382 T12: -0.0523 REMARK 3 T13: 0.0905 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: 0.2682 L22: 0.9499 REMARK 3 L33: 0.7222 L12: -0.1110 REMARK 3 L13: -0.0856 L23: -0.1924 REMARK 3 S TENSOR REMARK 3 S11: 0.0890 S12: 0.1559 S13: -0.0031 REMARK 3 S21: -0.3803 S22: 0.1385 S23: -0.3227 REMARK 3 S31: -0.1658 S32: 0.2325 S33: 0.1077 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 330:386 REMARK 3 ORIGIN FOR THE GROUP (A): -13.8226 20.1151 0.7226 REMARK 3 T TENSOR REMARK 3 T11: 0.1203 T22: 0.1226 REMARK 3 T33: 0.1245 T12: 0.0093 REMARK 3 T13: -0.0065 T23: -0.0221 REMARK 3 L TENSOR REMARK 3 L11: 0.6115 L22: 0.4735 REMARK 3 L33: 0.4687 L12: -0.0152 REMARK 3 L13: 0.0674 L23: -0.1952 REMARK 3 S TENSOR REMARK 3 S11: -0.0763 S12: -0.1283 S13: 0.0767 REMARK 3 S21: 0.0543 S22: 0.0966 S23: -0.0452 REMARK 3 S31: -0.0157 S32: -0.1277 S33: 0.0097 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 387:495 REMARK 3 ORIGIN FOR THE GROUP (A): -12.3492 -5.1860 -7.5442 REMARK 3 T TENSOR REMARK 3 T11: 0.1365 T22: 0.1022 REMARK 3 T33: 0.1745 T12: -0.0015 REMARK 3 T13: -0.0145 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.5596 L22: 0.5736 REMARK 3 L33: 1.3370 L12: -0.1197 REMARK 3 L13: 0.2823 L23: -0.1859 REMARK 3 S TENSOR REMARK 3 S11: 0.0482 S12: 0.0036 S13: -0.1654 REMARK 3 S21: 0.0300 S22: 0.0246 S23: 0.0383 REMARK 3 S31: 0.1549 S32: 0.0984 S33: 0.0090 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 496:575 REMARK 3 ORIGIN FOR THE GROUP (A): -19.8149 1.7438 -27.8374 REMARK 3 T TENSOR REMARK 3 T11: 0.2064 T22: 0.1815 REMARK 3 T33: 0.1426 T12: 0.0116 REMARK 3 T13: -0.0367 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 0.4188 L22: 0.3462 REMARK 3 L33: 0.9265 L12: -0.0565 REMARK 3 L13: 0.3262 L23: 0.1962 REMARK 3 S TENSOR REMARK 3 S11: 0.0009 S12: 0.1694 S13: -0.0330 REMARK 3 S21: -0.2324 S22: 0.0023 S23: 0.0494 REMARK 3 S31: -0.0664 S32: 0.0889 S33: 0.0212 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN U OR CHAIN P REMARK 3 ORIGIN FOR THE GROUP (A): -26.1170 10.2232 -9.0027 REMARK 3 T TENSOR REMARK 3 T11: 0.1351 T22: 0.1642 REMARK 3 T33: 0.1854 T12: -0.0075 REMARK 3 T13: 0.0136 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 0.2315 L22: 0.2636 REMARK 3 L33: 0.0360 L12: -0.3600 REMARK 3 L13: 0.1104 L23: 0.0312 REMARK 3 S TENSOR REMARK 3 S11: -0.0250 S12: 0.0865 S13: -0.0101 REMARK 3 S21: 0.0590 S22: -0.0024 S23: 0.1426 REMARK 3 S31: 0.0336 S32: -0.0485 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN T OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -23.8634 23.0958 -27.7462 REMARK 3 T TENSOR REMARK 3 T11: 0.2471 T22: 0.2351 REMARK 3 T33: 0.1567 T12: 0.0344 REMARK 3 T13: -0.0438 T23: 0.0350 REMARK 3 L TENSOR REMARK 3 L11: 0.1184 L22: 0.0549 REMARK 3 L33: 0.3322 L12: -0.0869 REMARK 3 L13: -0.2131 L23: 0.1208 REMARK 3 S TENSOR REMARK 3 S11: 0.1346 S12: 0.2249 S13: -0.0028 REMARK 3 S21: -0.1326 S22: -0.0133 S23: 0.0501 REMARK 3 S31: -0.1367 S32: -0.0835 S33: 0.0629 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 7M09 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 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) : 1.00 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(III) 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57424 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 20.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.80300 REMARK 200 FOR SHELL : 1.310 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2PFO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80MM NA CACODYLATE PH 6.5, 0.16MM REMARK 280 CALCIUM ACETATE, 14.4% (W/V) PEG 8000, 20% (V/V) GLYCEROL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 27.97050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.02100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.80750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.02100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.97050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.80750 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -107.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D, U 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 230 REMARK 465 SER A 231 REMARK 465 ALA A 232 REMARK 465 ALA A 233 REMARK 465 ALA A 234 REMARK 465 VAL A 235 REMARK 465 ARG A 538 REMARK 465 ASN A 539 REMARK 465 THR A 540 REMARK 465 HIS A 541 REMARK 465 GLY A 542 REMARK 465 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 465 GLY A 546 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 LEU A 236 CG CD1 CD2 REMARK 470 ASP A 237 CG OD1 OD2 REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 GLN A 243 OE1 NE2 REMARK 470 LYS A 259 CE NZ REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ARG A 308 CD NE CZ NH1 NH2 REMARK 470 GLU A 311 OE1 OE2 REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 HIS A 321 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 385 CD OE1 OE2 REMARK 470 GLU A 390 CD OE1 OE2 REMARK 470 LYS A 401 CD CE NZ REMARK 470 LEU A 411 CD1 CD2 REMARK 470 ARG A 438 NH1 NH2 REMARK 470 ARG A 441 CD NE CZ NH1 NH2 REMARK 470 ARG A 446 NE CZ NH1 NH2 REMARK 470 ASP A 449 CG OD1 OD2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 GLU A 454 CG CD OE1 OE2 REMARK 470 GLU A 466 CG CD OE1 OE2 REMARK 470 GLN A 469 OE1 NE2 REMARK 470 LYS A 523 NZ REMARK 470 VAL A 537 CG1 CG2 REMARK 470 LYS A 557 CD CE NZ REMARK 470 GLU A 569 CD OE1 OE2 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 OP2 DG D 1 O HOH D 101 2.16 REMARK 500 OE2 GLU A 394 O HOH A 801 2.17 REMARK 500 OP2 DG T 2 O HOH T 101 2.17 REMARK 500 O HOH A 1117 O HOH A 1136 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG T 2 O3' DG T 2 C3' -0.050 REMARK 500 DA P 2 O3' DA P 2 C3' -0.038 REMARK 500 DG D 1 P DG D 1 OP3 -0.121 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 T 2 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC D 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG U 6 O5' - P - OP2 ANGL. DEV. = -9.0 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 ASN A 251 105.36 -46.42 REMARK 500 CYS A 415 -139.03 -112.16 REMARK 500 SER A 463 94.73 -163.48 REMARK 500 ASP A 574 60.00 -92.50 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 A1142 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A1143 DISTANCE = 5.99 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 NA A 706 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 O REMARK 620 2 ILE A 302 O 98.4 REMARK 620 3 ILE A 305 O 91.8 85.5 REMARK 620 4 HOH A1027 O 86.6 87.9 172.9 REMARK 620 5 DC D 3 OP1 171.9 89.3 91.3 91.1 REMARK 620 6 HOH D 117 O 89.1 171.6 98.2 88.6 83.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 705 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 99.9 REMARK 620 3 ALA A 344 O 89.7 85.9 REMARK 620 4 HOH A1054 O 87.0 93.7 176.5 REMARK 620 5 DG P 5 OP1 163.9 96.1 92.5 91.0 REMARK 620 6 HOH P 209 O 73.0 169.1 85.7 94.2 91.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD1 99.9 REMARK 620 3 ASP A 490 OD2 89.2 101.1 REMARK 620 4 DUP A 701 O2A 95.7 87.9 168.9 REMARK 620 5 HOH A 878 O 81.5 166.7 92.1 78.8 REMARK 620 6 DC P 6 O3' 163.6 91.7 77.1 96.2 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD1 99.9 REMARK 620 3 ASP A 490 OD2 89.2 101.1 REMARK 620 4 DUP A 701 O2A 95.7 87.9 168.9 REMARK 620 5 HOH A 878 O 81.5 166.7 92.1 78.8 REMARK 620 6 DC P 6 O3' 163.6 91.7 77.1 96.2 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 704 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 96.9 REMARK 620 3 DUP A 701 O2A 97.4 89.7 REMARK 620 4 DUP A 701 O2B 168.5 90.8 91.1 REMARK 620 5 DUP A 701 O3G 86.8 176.2 90.0 85.5 REMARK 620 6 HOH A 923 O 85.2 88.7 177.1 86.4 91.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 709 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUP A 701 O1G REMARK 620 2 HOH A 833 O 88.3 REMARK 620 3 HOH A 839 O 123.7 112.8 REMARK 620 4 HOH A 843 O 86.6 73.8 54.7 REMARK 620 5 HOH A1022 O 88.4 95.1 136.3 168.0 REMARK 620 6 HOH A1053 O 95.9 175.7 64.3 105.9 85.5 REMARK 620 7 HOH A1135 O 171.8 87.3 52.4 85.5 98.8 88.4 REMARK 620 N 1 2 3 4 5 6 DBREF 7M09 A 234 575 UNP Q9UGP5 DPOLL_HUMAN 234 575 DBREF 7M09 T 1 5 PDB 7M09 7M09 1 5 DBREF 7M09 P 1 6 PDB 7M09 7M09 1 6 DBREF 7M09 D 1 4 PDB 7M09 7M09 1 4 DBREF 7M09 U 1 6 PDB 7M09 7M09 1 6 SEQADV 7M09 GLY A 230 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M09 SER A 231 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M09 ALA A 232 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M09 ALA A 233 UNP Q9UGP5 EXPRESSION TAG SEQRES 1 A 346 GLY SER ALA ALA ALA VAL LEU ASP LYS TRP VAL CYS ALA SEQRES 2 A 346 GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU HIS SEQRES 3 A 346 ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SER SEQRES 4 A 346 VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA LYS SEQRES 5 A 346 ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL THR SEQRES 6 A 346 SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY LYS SEQRES 7 A 346 ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER GLY SEQRES 8 A 346 HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL PRO SEQRES 9 A 346 VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY THR SEQRES 10 A 346 LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SER SEQRES 11 A 346 LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR GLN SEQRES 12 A 346 GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU GLU SEQRES 13 A 346 ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN THR SEQRES 14 A 346 VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU LEU SEQRES 15 A 346 CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA THR SEQRES 16 A 346 CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP GLY SEQRES 17 A 346 ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SER SEQRES 18 A 346 LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SER SEQRES 19 A 346 GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU GLY VAL SEQRES 20 A 346 CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG ARG LEU SEQRES 21 A 346 ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA CYS ALA SEQRES 22 A 346 LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN ARG SER SEQRES 23 A 346 MET ARG ALA LEU ALA LYS THR LYS GLY MET SER LEU SER SEQRES 24 A 346 GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN THR HIS SEQRES 25 A 346 GLY CYS LYS VAL GLY PRO GLY ARG VAL LEU PRO THR PRO SEQRES 26 A 346 THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU PRO TYR SEQRES 27 A 346 ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 T 5 DC DG DG DC DA SEQRES 1 P 6 DC DA DG DT DG DC SEQRES 1 D 4 DG DC DC DG SEQRES 1 U 6 DG DC DA DC DT DG HET DUP A 701 28 HET CA A 702 1 HET MG A 703 1 HET MG A 704 1 HET NA A 705 1 HET NA A 706 1 HET CL A 707 1 HET CL A 708 1 HET NA A 709 1 HET GOL A 710 6 HET GOL P 101 6 HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM CA CALCIUM ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 6 DUP C9 H16 N3 O13 P3 FORMUL 7 CA CA 2+ FORMUL 8 MG 2(MG 2+) FORMUL 10 NA 3(NA 1+) FORMUL 12 CL 2(CL 1-) FORMUL 15 GOL 2(C3 H8 O3) FORMUL 17 HOH *442(H2 O) HELIX 1 AA1 TRP A 239 GLN A 243 5 5 HELIX 2 AA2 PRO A 244 ASN A 251 5 8 HELIX 3 AA3 ASN A 253 GLY A 271 1 19 HELIX 4 AA4 ASP A 272 PHE A 289 1 18 HELIX 5 AA5 SER A 295 ILE A 302 1 8 HELIX 6 AA6 GLY A 306 GLY A 320 1 15 HELIX 7 AA7 LEU A 322 HIS A 327 5 6 HELIX 8 AA8 SER A 331 ASN A 340 1 10 HELIX 9 AA9 GLY A 345 GLN A 355 1 11 HELIX 10 AB1 SER A 359 ALA A 367 1 9 HELIX 11 AB2 THR A 370 HIS A 379 1 10 HELIX 12 AB3 HIS A 379 GLU A 385 1 7 HELIX 13 AB4 ARG A 389 ALA A 405 1 17 HELIX 14 AB5 CYS A 415 ARG A 420 1 6 HELIX 15 AB6 GLY A 442 GLU A 454 1 13 HELIX 16 AB7 PRO A 495 SER A 497 5 3 HELIX 17 AB8 GLU A 498 GLY A 508 1 11 HELIX 18 AB9 SER A 509 LYS A 523 1 15 HELIX 19 AC1 THR A 555 LEU A 563 1 9 HELIX 20 AC2 GLU A 569 ASP A 574 5 6 SHEET 1 AA1 2 MET A 387 PRO A 388 0 SHEET 2 AA1 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 AA2 5 LEU A 411 ALA A 414 0 SHEET 2 AA2 5 ASP A 427 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 AA2 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N CYS A 477 O ARG A 487 SHEET 5 AA2 5 LEU A 457 VAL A 462 -1 N VAL A 462 O LEU A 474 SHEET 1 AA3 2 MET A 525 LEU A 527 0 SHEET 2 AA3 2 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 LINK O CYS A 300 NA NA A 706 1555 1555 2.41 LINK O ILE A 302 NA NA A 706 1555 1555 2.54 LINK O ILE A 305 NA NA A 706 1555 1555 2.35 LINK O SER A 339 NA NA A 705 1555 1555 2.26 LINK O ILE A 341 NA NA A 705 1555 1555 2.43 LINK O ALA A 344 NA NA A 705 1555 1555 2.30 LINK OD2 ASP A 427 CA A CA A 702 1555 1555 2.04 LINK OD2 ASP A 427 MG B MG A 703 1555 1555 2.04 LINK OD1 ASP A 427 MG MG A 704 1555 1555 2.00 LINK OD1 ASP A 429 CA A CA A 702 1555 1555 2.07 LINK OD1 ASP A 429 MG B MG A 703 1555 1555 2.07 LINK OD2 ASP A 429 MG MG A 704 1555 1555 2.03 LINK OD2 ASP A 490 CA A CA A 702 1555 1555 2.07 LINK OD2 ASP A 490 MG B MG A 703 1555 1555 2.07 LINK O2A DUP A 701 CA A CA A 702 1555 1555 2.29 LINK O2A DUP A 701 MG B MG A 703 1555 1555 2.29 LINK O2A DUP A 701 MG MG A 704 1555 1555 2.15 LINK O2B DUP A 701 MG MG A 704 1555 1555 2.10 LINK O3G DUP A 701 MG MG A 704 1555 1555 2.12 LINK O1G DUP A 701 NA NA A 709 1555 1555 2.23 LINK CA A CA A 702 O HOH A 878 1555 1555 2.30 LINK CA A CA A 702 O3' DC P 6 1555 1555 2.32 LINK MG B MG A 703 O HOH A 878 1555 1555 2.30 LINK MG B MG A 703 O3' DC P 6 1555 1555 2.32 LINK MG MG A 704 O HOH A 923 1555 1555 2.13 LINK NA NA A 705 O HOH A1054 1555 1555 2.44 LINK NA NA A 705 OP1 DG P 5 1555 1555 2.37 LINK NA NA A 705 O HOH P 209 1555 1555 2.82 LINK NA NA A 706 O HOH A1027 1555 1555 2.47 LINK NA NA A 706 OP1 DC D 3 1555 1555 2.80 LINK NA NA A 706 O HOH D 117 1555 1555 2.91 LINK NA NA A 709 O HOH A 833 1555 1555 2.44 LINK NA NA A 709 O BHOH A 839 1555 1555 3.11 LINK NA NA A 709 O HOH A 843 1555 1555 2.64 LINK NA NA A 709 O HOH A1022 1555 1555 2.13 LINK NA NA A 709 O HOH A1053 1555 1555 2.12 LINK NA NA A 709 O HOH A1135 1555 1555 2.48 CISPEP 1 GLY A 508 SER A 509 0 1.08 CRYST1 55.941 59.615 140.042 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 0.017876 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016774 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007141 0.00000