HEADER TRANSFERASE/DNA 19-JAN-15 4XQ8 TITLE HUMAN DNA POLYMERASE LAMBDA- MGDATP BINARY COMPLEX AND COMPLEX WITH 6 TITLE 2 PAIRED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: B, A; COMPND 4 FRAGMENT: UNP RESIDUES 242-575; COMPND 5 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 6 KAPPA; COMPND 7 EC: 2.7.7.7; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'); COMPND 11 CHAIN: P; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3'); COMPND 15 CHAIN: T; COMPND 16 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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS COMPLEX, MGDATP, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.D.TSAI,M.S.LIU REVDAT 4 16-OCT-24 4XQ8 1 REMARK REVDAT 3 08-NOV-23 4XQ8 1 REMARK REVDAT 2 09-MAR-16 4XQ8 1 JRNL REVDAT 1 24-FEB-16 4XQ8 0 JRNL AUTH M.S.LIU,H.Y.TSAI,X.X.LIU,M.C.HO,W.J.WU,M.D.TSAI JRNL TITL STRUCTURAL MECHANISM FOR THE FIDELITY MODULATION OF DNA JRNL TITL 2 POLYMERASE LAMBDA JRNL REF J.AM.CHEM.SOC. V. 138 2389 2016 JRNL REFN ESSN 1520-5126 JRNL PMID 26836966 JRNL DOI 10.1021/JACS.5B13368 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 17909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.220 REMARK 3 FREE R VALUE TEST SET COUNT : 1652 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 27.4126 - 8.0065 0.99 1461 150 0.1536 0.1875 REMARK 3 2 8.0065 - 6.3814 1.00 1459 145 0.1568 0.1995 REMARK 3 3 6.3814 - 5.5825 1.00 1441 142 0.1617 0.1801 REMARK 3 4 5.5825 - 5.0756 1.00 1494 153 0.1637 0.1991 REMARK 3 5 5.0756 - 4.7137 1.00 1440 148 0.1375 0.2029 REMARK 3 6 4.7137 - 4.4371 1.00 1456 145 0.1475 0.2474 REMARK 3 7 4.4371 - 4.2157 1.00 1463 149 0.1545 0.2050 REMARK 3 8 4.2157 - 4.0328 1.00 1453 150 0.1504 0.1987 REMARK 3 9 4.0328 - 3.8780 1.00 1466 152 0.1661 0.2320 REMARK 3 10 3.8780 - 3.7445 1.00 1471 154 0.1774 0.2297 REMARK 3 11 3.7445 - 3.6277 1.00 1405 141 0.1881 0.2718 REMARK 3 12 3.6277 - 3.5242 1.00 1491 157 0.1876 0.2785 REMARK 3 13 3.5242 - 3.4316 1.00 1462 150 0.2032 0.2450 REMARK 3 14 3.4316 - 3.3480 1.00 1431 149 0.2114 0.2542 REMARK 3 15 3.3480 - 3.2720 1.00 1493 150 0.2150 0.3042 REMARK 3 16 3.2720 - 3.2025 1.00 1432 148 0.2350 0.2723 REMARK 3 17 3.2025 - 3.1385 0.98 1444 149 0.2358 0.3493 REMARK 3 18 3.1385 - 3.0794 0.92 1330 135 0.2560 0.3555 REMARK 3 19 3.0794 - 3.0245 0.86 1243 124 0.2442 0.3295 REMARK 3 20 3.0245 - 2.9733 0.81 1189 112 0.2378 0.2688 REMARK 3 21 2.9733 - 2.9254 0.74 1093 110 0.2392 0.3063 REMARK 3 22 2.9254 - 2.8804 0.71 1022 104 0.2233 0.2531 REMARK 3 23 2.8804 - 2.8381 0.66 985 98 0.2410 0.3254 REMARK 3 24 2.8381 - 2.7981 0.62 890 88 0.2513 0.2752 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.009 4247 REMARK 3 ANGLE : 1.183 5790 REMARK 3 CHIRALITY : 0.043 627 REMARK 3 PLANARITY : 0.006 713 REMARK 3 DIHEDRAL : 17.617 1607 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4XQ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000206111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21679 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.798 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.49100 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: 4W5D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M HEPES-SODIUM, 0.1 M POTASSIUM SODIUM TARTRATE, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 265.83067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 132.91533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 199.37300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 66.45767 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 332.28833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 265.83067 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 132.91533 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 66.45767 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 199.37300 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 332.28833 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, P, T 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 ALA B 242 REMARK 465 GLN B 243 REMARK 465 PRO B 244 REMARK 465 SER B 245 REMARK 465 SER B 246 REMARK 465 GLN B 247 REMARK 465 LYS B 248 REMARK 465 ALA B 249 REMARK 465 THR B 250 REMARK 465 ASN B 251 REMARK 465 HIS B 252 REMARK 465 ASN B 253 REMARK 465 LEU B 254 REMARK 465 HIS B 255 REMARK 465 ILE B 256 REMARK 465 THR B 257 REMARK 465 GLU B 258 REMARK 465 LYS B 259 REMARK 465 LEU B 260 REMARK 465 GLU B 261 REMARK 465 VAL B 262 REMARK 465 LEU B 263 REMARK 465 ALA B 264 REMARK 465 LYS B 265 REMARK 465 ALA B 266 REMARK 465 TYR B 267 REMARK 465 SER B 268 REMARK 465 VAL B 269 REMARK 465 GLN B 270 REMARK 465 GLY B 271 REMARK 465 ASP B 272 REMARK 465 LYS B 273 REMARK 465 TRP B 274 REMARK 465 ARG B 275 REMARK 465 ALA B 276 REMARK 465 LEU B 277 REMARK 465 GLY B 278 REMARK 465 TYR B 279 REMARK 465 ALA B 280 REMARK 465 LYS B 281 REMARK 465 ALA B 282 REMARK 465 ILE B 283 REMARK 465 ASN B 284 REMARK 465 ALA B 285 REMARK 465 LEU B 286 REMARK 465 LYS B 287 REMARK 465 SER B 288 REMARK 465 PHE B 289 REMARK 465 HIS B 290 REMARK 465 LYS B 291 REMARK 465 PRO B 292 REMARK 465 VAL B 293 REMARK 465 THR B 294 REMARK 465 SER B 295 REMARK 465 TYR B 296 REMARK 465 GLN B 297 REMARK 465 GLU B 298 REMARK 465 ALA B 299 REMARK 465 CYS B 300 REMARK 465 SER B 301 REMARK 465 ILE B 302 REMARK 465 PRO B 303 REMARK 465 GLY B 304 REMARK 465 ILE B 305 REMARK 465 GLY B 306 REMARK 465 LYS B 307 REMARK 465 ARG B 308 REMARK 465 MET B 309 REMARK 465 ALA B 310 REMARK 465 GLU B 311 REMARK 465 LYS B 312 REMARK 465 ILE B 313 REMARK 465 ILE B 314 REMARK 465 GLU B 315 REMARK 465 ILE B 316 REMARK 465 LEU B 317 REMARK 465 GLU B 318 REMARK 465 SER B 319 REMARK 465 GLY B 320 REMARK 465 HIS B 321 REMARK 465 LEU B 322 REMARK 465 ARG B 323 REMARK 465 LYS B 324 REMARK 465 LEU B 325 REMARK 465 ASP B 326 REMARK 465 HIS B 327 REMARK 465 ILE B 328 REMARK 465 ALA A 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 465 ALA A 249 REMARK 465 THR A 250 REMARK 465 ASN A 251 REMARK 465 HIS A 252 REMARK 465 ASN A 253 REMARK 465 LEU A 254 REMARK 465 HIS A 255 REMARK 465 ILE A 256 REMARK 465 THR A 257 REMARK 465 GLU A 258 REMARK 465 LYS A 259 REMARK 465 LEU A 260 REMARK 465 GLU A 261 REMARK 465 VAL A 262 REMARK 465 LEU A 263 REMARK 465 ALA A 264 REMARK 465 LYS A 265 REMARK 465 ALA A 266 REMARK 465 TYR A 267 REMARK 465 SER A 268 REMARK 465 VAL A 269 REMARK 465 GLN A 270 REMARK 465 GLY A 271 REMARK 465 ASP A 272 REMARK 465 LYS A 273 REMARK 465 TRP A 274 REMARK 465 ARG A 275 REMARK 465 ALA A 276 REMARK 465 LEU A 277 REMARK 465 GLY A 278 REMARK 465 TYR A 279 REMARK 465 ALA A 280 REMARK 465 LYS A 281 REMARK 465 ALA A 282 REMARK 465 ILE A 283 REMARK 465 ASN A 284 REMARK 465 ALA A 285 REMARK 465 LEU A 286 REMARK 465 LYS A 287 REMARK 465 SER A 288 REMARK 465 PHE A 289 REMARK 465 HIS A 290 REMARK 465 LYS A 291 REMARK 465 PRO A 292 REMARK 465 VAL A 293 REMARK 465 THR A 294 REMARK 465 SER A 295 REMARK 465 TYR A 296 REMARK 465 GLN A 297 REMARK 465 GLU A 298 REMARK 465 ALA A 299 REMARK 465 CYS A 300 REMARK 465 SER A 301 REMARK 465 ILE A 302 REMARK 465 PRO A 303 REMARK 465 GLY A 304 REMARK 465 ILE A 305 REMARK 465 GLY A 306 REMARK 465 LYS A 307 REMARK 465 ARG A 308 REMARK 465 MET A 309 REMARK 465 ALA A 310 REMARK 465 GLU A 311 REMARK 465 LYS A 312 REMARK 465 ILE A 313 REMARK 465 ILE A 314 REMARK 465 GLU A 315 REMARK 465 ILE A 316 REMARK 465 LEU A 317 REMARK 465 GLU A 318 REMARK 465 SER A 319 REMARK 465 GLY A 320 REMARK 465 HIS A 321 REMARK 465 LEU A 322 REMARK 465 ARG A 323 REMARK 465 LYS A 324 REMARK 465 LEU A 325 REMARK 465 ASP A 326 REMARK 465 HIS A 327 REMARK 465 ILE A 328 REMARK 465 SER A 329 REMARK 465 GLU A 330 REMARK 465 SER A 331 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 OD2 ASP B 436 OG SER B 439 1.84 REMARK 500 O LEU B 519 OG1 THR B 522 2.06 REMARK 500 O HOH A 716 O HOH A 727 2.06 REMARK 500 OP2 DG T 6 O HOH T 101 2.09 REMARK 500 O HOH A 736 O HOH A 747 2.13 REMARK 500 OG SER A 417 O1G DTP A 601 2.14 REMARK 500 O HOH B 615 O HOH P 104 2.15 REMARK 500 O SER A 339 O HOH A 701 2.16 REMARK 500 O ALA A 344 O HOH A 701 2.17 REMARK 500 O ARG B 485 O HOH B 601 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER B 331 OE1 GLU A 390 12564 2.03 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 DC P 1 O3' DC P 1 C3' -0.036 REMARK 500 DC T 9 O3' DC T 9 C3' -0.047 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 P 3 O4' - C1' - N9 ANGL. DEV. = 1.8 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 CYS B 415 -142.68 -112.73 REMARK 500 CYS A 415 -154.64 -113.05 REMARK 500 ARG A 438 -52.67 -123.25 REMARK 500 REMARK 500 REMARK: NULL 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 A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 100.8 REMARK 620 3 DTP A 601 O2G 85.0 174.1 REMARK 620 4 DTP A 601 O2B 149.8 109.3 64.8 REMARK 620 5 DTP A 601 O2A 96.4 102.7 75.4 74.9 REMARK 620 6 HOH A 707 O 89.9 108.4 72.4 83.2 146.5 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 DTP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 DBREF 4XQ8 B 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 4XQ8 A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 4XQ8 P 1 6 PDB 4XQ8 4XQ8 1 6 DBREF 4XQ8 T 6 11 PDB 4XQ8 4XQ8 6 11 SEQRES 1 B 334 ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU SEQRES 2 B 334 HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SEQRES 3 B 334 SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA SEQRES 4 B 334 LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL SEQRES 5 B 334 THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY SEQRES 6 B 334 LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER SEQRES 7 B 334 GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL SEQRES 8 B 334 PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY SEQRES 9 B 334 THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SEQRES 10 B 334 SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR SEQRES 11 B 334 GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU SEQRES 12 B 334 GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN SEQRES 13 B 334 THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU SEQRES 14 B 334 LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA SEQRES 15 B 334 THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP SEQRES 16 B 334 GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SEQRES 17 B 334 SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SEQRES 18 B 334 SER GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU GLY SEQRES 19 B 334 VAL CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG ARG SEQRES 20 B 334 LEU ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA CYS SEQRES 21 B 334 ALA LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN ARG SEQRES 22 B 334 SER MET ARG ALA LEU ALA LYS THR LYS GLY MET SER LEU SEQRES 23 B 334 SER GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN THR SEQRES 24 B 334 HIS GLY CYS LYS VAL GLY PRO GLY ARG VAL LEU PRO THR SEQRES 25 B 334 PRO THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU PRO SEQRES 26 B 334 TYR ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 A 334 ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU SEQRES 2 A 334 HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SEQRES 3 A 334 SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA SEQRES 4 A 334 LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL SEQRES 5 A 334 THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY SEQRES 6 A 334 LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER SEQRES 7 A 334 GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL SEQRES 8 A 334 PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY SEQRES 9 A 334 THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SEQRES 10 A 334 SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR SEQRES 11 A 334 GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU SEQRES 12 A 334 GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN SEQRES 13 A 334 THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU SEQRES 14 A 334 LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA SEQRES 15 A 334 THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP SEQRES 16 A 334 GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SEQRES 17 A 334 SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SEQRES 18 A 334 SER GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU GLY SEQRES 19 A 334 VAL CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG ARG SEQRES 20 A 334 LEU ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA CYS SEQRES 21 A 334 ALA LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN ARG SEQRES 22 A 334 SER MET ARG ALA LEU ALA LYS THR LYS GLY MET SER LEU SEQRES 23 A 334 SER GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN THR SEQRES 24 A 334 HIS GLY CYS LYS VAL GLY PRO GLY ARG VAL LEU PRO THR SEQRES 25 A 334 PRO THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU PRO SEQRES 26 A 334 TYR ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 P 6 DC DA DG DT DA DC SEQRES 1 T 6 DG DT DA DC DT DG HET DTP A 601 30 HET MG A 602 1 HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 5 DTP C10 H16 N5 O12 P3 FORMUL 6 MG MG 2+ FORMUL 7 HOH *99(H2 O) HELIX 1 AA1 GLU B 330 ASN B 340 1 11 HELIX 2 AA2 GLY B 345 GLN B 355 1 11 HELIX 3 AA3 SER B 359 ALA B 367 1 9 HELIX 4 AA4 THR B 370 HIS B 379 1 10 HELIX 5 AA5 HIS B 379 GLU B 385 1 7 HELIX 6 AA6 ARG B 389 ASN B 407 1 19 HELIX 7 AA7 CYS B 415 ARG B 420 1 6 HELIX 8 AA8 ILE B 443 GLU B 454 1 12 HELIX 9 AA9 PRO B 495 SER B 497 5 3 HELIX 10 AB1 GLU B 498 GLY B 508 1 11 HELIX 11 AB2 SER B 509 LYS B 523 1 15 HELIX 12 AB3 THR B 555 LEU B 563 1 9 HELIX 13 AB4 GLU B 569 ARG B 573 5 5 HELIX 14 AB5 PRO A 333 ASN A 340 1 8 HELIX 15 AB6 GLY A 345 GLN A 355 1 11 HELIX 16 AB7 SER A 359 ALA A 367 1 9 HELIX 17 AB8 THR A 370 HIS A 379 1 10 HELIX 18 AB9 HIS A 379 LEU A 384 1 6 HELIX 19 AC1 ARG A 389 ALA A 405 1 17 HELIX 20 AC2 ILE A 443 GLU A 454 1 12 HELIX 21 AC3 PRO A 495 SER A 497 5 3 HELIX 22 AC4 GLU A 498 GLY A 508 1 11 HELIX 23 AC5 SER A 509 LYS A 523 1 15 HELIX 24 AC6 THR A 555 GLY A 564 1 10 HELIX 25 AC7 GLU A 569 ARG A 573 5 5 SHEET 1 AA1 2 MET B 387 PRO B 388 0 SHEET 2 AA1 2 THR B 424 CYS B 425 -1 O CYS B 425 N MET B 387 SHEET 1 AA2 5 LEU B 411 ALA B 414 0 SHEET 2 AA2 5 ASP B 427 THR B 433 -1 O THR B 433 N LEU B 411 SHEET 3 AA2 5 ARG B 487 VAL B 493 1 O ASP B 490 N VAL B 430 SHEET 4 AA2 5 GLN B 470 CYS B 477 -1 N CYS B 477 O ARG B 487 SHEET 5 AA2 5 LEU B 457 ASN B 467 -1 N THR B 458 O VAL B 476 SHEET 1 AA3 3 SER B 526 LEU B 527 0 SHEET 2 AA3 3 LEU B 532 THR B 534 -1 O SER B 533 N SER B 526 SHEET 3 AA3 3 ARG B 549 LEU B 551 -1 O ARG B 549 N THR B 534 SHEET 1 AA4 2 VAL B 537 ARG B 538 0 SHEET 2 AA4 2 LYS B 544 GLY B 546 -1 O VAL B 545 N VAL B 537 SHEET 1 AA5 2 MET A 387 PRO A 388 0 SHEET 2 AA5 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 AA6 5 LEU A 411 CYS A 415 0 SHEET 2 AA6 5 ASP A 427 THR A 433 -1 O THR A 433 N LEU A 411 SHEET 3 AA6 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 AA6 5 GLN A 470 CYS A 477 -1 N GLY A 475 O LEU A 489 SHEET 5 AA6 5 LEU A 457 ASN A 467 -1 N THR A 458 O VAL A 476 SHEET 1 AA7 2 MET A 525 LEU A 527 0 SHEET 2 AA7 2 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 1 AA8 2 VAL A 537 ARG A 538 0 SHEET 2 AA8 2 LYS A 544 GLY A 546 -1 O VAL A 545 N VAL A 537 SSBOND 1 CYS B 543 CYS A 543 1555 5565 2.05 LINK OD1 ASP A 427 MG MG A 602 1555 1555 1.77 LINK OD2 ASP A 429 MG MG A 602 1555 1555 1.71 LINK O2G DTP A 601 MG MG A 602 1555 1555 2.68 LINK O2B DTP A 601 MG MG A 602 1555 1555 1.90 LINK O2A DTP A 601 MG MG A 602 1555 1555 2.27 LINK MG MG A 602 O HOH A 707 1555 1555 1.82 CISPEP 1 GLY B 508 SER B 509 0 -1.05 CISPEP 2 GLY A 508 SER A 509 0 5.51 SITE 1 AC1 14 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC1 14 GLY A 426 ASP A 427 ASP A 429 TYR A 505 SITE 3 AC1 14 PHE A 506 GLY A 508 ASN A 513 MG A 602 SITE 4 AC1 14 HOH A 707 HOH A 714 SITE 1 AC2 4 ASP A 427 ASP A 429 DTP A 601 HOH A 707 CRYST1 83.743 83.743 398.746 90.00 90.00 120.00 P 65 2 2 24 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 0.011941 0.006894 0.000000 0.00000 SCALE2 0.000000 0.013789 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002508 0.00000