PDB Short entry for 5DDM HEADER TRANSFERASE/DNA 18-AUG-14 5DDM TITLE HUMAN DNA POLYMERASE LAMBDA- APOENZYME AND COMPLEX WITH 6 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 DNA POLYMERASE LAMBDA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.S.LIU,M.D.TSAI REVDAT 3 08-NOV-23 5DDM 1 REMARK LINK REVDAT 2 09-MAR-16 5DDM 1 JRNL REVDAT 1 24-FEB-16 5DDM 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 (PHENIX.REFINE: 1.8.1_1168) 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) : 27.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21267 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 27.9840 - 6.7245 0.99 1553 161 0.1890 0.1981 REMARK 3 2 6.7245 - 5.3496 0.99 1429 149 0.1930 0.2181 REMARK 3 3 5.3496 - 4.6770 0.99 1391 144 0.1719 0.2070 REMARK 3 4 4.6770 - 4.2510 1.00 1391 145 0.1690 0.2241 REMARK 3 5 4.2510 - 3.9472 1.00 1375 143 0.1695 0.2126 REMARK 3 6 3.9472 - 3.7150 1.00 1381 143 0.2001 0.2270 REMARK 3 7 3.7150 - 3.5293 1.00 1353 140 0.2036 0.2400 REMARK 3 8 3.5293 - 3.3760 1.00 1356 141 0.2124 0.2593 REMARK 3 9 3.3760 - 3.2462 1.00 1349 140 0.2260 0.3211 REMARK 3 10 3.2462 - 3.1343 1.00 1362 141 0.2600 0.2645 REMARK 3 11 3.1343 - 3.0364 1.00 1336 139 0.2503 0.2883 REMARK 3 12 3.0364 - 2.9497 1.00 1340 138 0.2477 0.3040 REMARK 3 13 2.9497 - 2.8722 1.00 1323 138 0.2386 0.3077 REMARK 3 14 2.8722 - 2.8022 1.00 1328 138 0.2447 0.2958 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.23 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 : 0.008 4204 REMARK 3 ANGLE : 1.175 5724 REMARK 3 CHIRALITY : 0.074 621 REMARK 3 PLANARITY : 0.005 709 REMARK 3 DIHEDRAL : 17.582 1585 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 5DDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000213059. 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 : 7.5 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, HKL REMARK 200 DATA SCALING SOFTWARE : HKL-2000, HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21271 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.0000 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 : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.50400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 1XSL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M LITHIUM SULFATE MONOHYDRATE, 0.1M REMARK 280 HEPES-SODIUM, 0.1M POTASSIUM SODIUM TARTRATE, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 264.21733 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 132.10867 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 198.16300 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 66.05433 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 330.27167 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 264.21733 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 132.10867 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 66.05433 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 198.16300 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 330.27167 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: 2970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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: 200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 MET B 241 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 MET A 241 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 465 VAL A 332 REMARK 465 PRO A 333 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 NH1 ARG B 420 OD1 ASP B 574 1.96 REMARK 500 OG1 THR B 507 O HOH B 701 2.11 REMARK 500 O GLU B 465 O HOH B 702 2.13 REMARK 500 OE1 GLN B 471 O HOH B 703 2.15 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 CYS B 415 CB CYS B 415 SG -0.112 REMARK 500 TYR A 418 CE2 TYR A 418 CD2 -0.094 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 P 1 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT P 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC P 6 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 DC P 6 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA T 8 O4' - C1' - N9 ANGL. DEV. = 5.6 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 -162.53 -122.19 REMARK 500 CYS A 415 -165.22 -123.73 REMARK 500 ARG A 573 30.23 -99.10 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 NA B 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 339 O REMARK 620 2 ILE B 341 O 86.7 REMARK 620 3 ALA B 344 O 82.6 69.4 REMARK 620 4 DT P 4 OP1 162.3 82.4 80.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DDY RELATED DB: PDB REMARK 900 5DDY CONTAINS THE SAME PROTEIN COMPLEXED WITH MNMGDCTP DBREF 5DDM B 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 5DDM A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 5DDM P 1 6 PDB 5DDM 5DDM 1 6 DBREF 5DDM T 6 11 PDB 5DDM 5DDM 6 11 SEQADV 5DDM MET B 241 UNP Q9UGP5 EXPRESSION TAG SEQADV 5DDM MET A 241 UNP Q9UGP5 EXPRESSION TAG SEQRES 1 B 335 MET ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN SEQRES 2 B 335 LEU HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA SEQRES 3 B 335 TYR SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR SEQRES 4 B 335 ALA LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO SEQRES 5 B 335 VAL THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE SEQRES 6 B 335 GLY LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SEQRES 7 B 335 SER GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER SEQRES 8 B 335 VAL PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA SEQRES 9 B 335 GLY THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE SEQRES 10 B 335 ARG SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR SEQRES 11 B 335 THR GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE SEQRES 12 B 335 LEU GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU SEQRES 13 B 335 GLN THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY SEQRES 14 B 335 LEU LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS SEQRES 15 B 335 ALA THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO SEQRES 16 B 335 ASP GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU SEQRES 17 B 335 ASP SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU SEQRES 18 B 335 VAL SER GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU SEQRES 19 B 335 GLY VAL CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG SEQRES 20 B 335 ARG LEU ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA SEQRES 21 B 335 CYS ALA LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN SEQRES 22 B 335 ARG SER MET ARG ALA LEU ALA LYS THR LYS GLY MET SER SEQRES 23 B 335 LEU SER GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN SEQRES 24 B 335 THR HIS GLY CYS LYS VAL GLY PRO GLY ARG VAL LEU PRO SEQRES 25 B 335 THR PRO THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU SEQRES 26 B 335 PRO TYR ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 A 335 MET ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN SEQRES 2 A 335 LEU HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA SEQRES 3 A 335 TYR SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR SEQRES 4 A 335 ALA LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO SEQRES 5 A 335 VAL THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE SEQRES 6 A 335 GLY LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SEQRES 7 A 335 SER GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER SEQRES 8 A 335 VAL PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA SEQRES 9 A 335 GLY THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE SEQRES 10 A 335 ARG SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR SEQRES 11 A 335 THR GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE SEQRES 12 A 335 LEU GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU SEQRES 13 A 335 GLN THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY SEQRES 14 A 335 LEU LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS SEQRES 15 A 335 ALA THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO SEQRES 16 A 335 ASP GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU SEQRES 17 A 335 ASP SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU SEQRES 18 A 335 VAL SER GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU SEQRES 19 A 335 GLY VAL CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG SEQRES 20 A 335 ARG LEU ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA SEQRES 21 A 335 CYS ALA LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN SEQRES 22 A 335 ARG SER MET ARG ALA LEU ALA LYS THR LYS GLY MET SER SEQRES 23 A 335 LEU SER GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN SEQRES 24 A 335 THR HIS GLY CYS LYS VAL GLY PRO GLY ARG VAL LEU PRO SEQRES 25 A 335 THR PRO THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU SEQRES 26 A 335 PRO 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 NA B 601 1 HET SO4 A 601 5 HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION FORMUL 5 NA NA 1+ FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *69(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 ALA B 405 1 17 HELIX 7 AA7 GLY B 416 GLY B 421 1 6 HELIX 8 AA8 GLY B 442 GLU B 454 1 13 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 GLY A 345 GLN A 355 1 11 HELIX 15 AB6 SER A 359 ALA A 367 1 9 HELIX 16 AB7 THR A 370 HIS A 379 1 10 HELIX 17 AB8 HIS A 379 LEU A 384 1 6 HELIX 18 AB9 ARG A 389 ASN A 407 1 19 HELIX 19 AC1 GLY A 442 GLU A 454 1 13 HELIX 20 AC2 PRO A 495 SER A 497 5 3 HELIX 21 AC3 GLU A 498 GLY A 508 1 11 HELIX 22 AC4 SER A 509 LYS A 523 1 15 HELIX 23 AC5 THR A 555 GLY A 564 1 10 HELIX 24 AC6 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 CYS B 415 0 SHEET 2 AA2 5 VAL B 428 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 VAL B 462 O LEU B 474 SHEET 1 AA3 3 MET B 525 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 LEU B 551 N LEU B 532 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 VAL A 428 THR A 433 -1 O THR A 433 N LEU A 411 SHEET 3 AA6 5 ARG A 487 VAL A 493 1 O ILE A 492 N ILE A 432 SHEET 4 AA6 5 GLN A 470 CYS A 477 -1 N CYS A 477 O ARG A 487 SHEET 5 AA6 5 LEU A 457 ASN A 467 -1 N LEU A 461 O LEU A 474 SHEET 1 AA7 3 MET A 525 LEU A 527 0 SHEET 2 AA7 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 AA7 3 VAL A 550 LEU A 551 -1 O LEU A 551 N LEU A 532 SSBOND 1 CYS B 543 CYS A 543 1555 6664 2.04 LINK O SER B 339 NA NA B 601 1555 1555 2.31 LINK O ILE B 341 NA NA B 601 1555 1555 2.79 LINK O ALA B 344 NA NA B 601 1555 1555 2.63 LINK NA NA B 601 OP1 DT P 4 1555 1555 2.76 CISPEP 1 GLY B 508 SER B 509 0 5.29 CISPEP 2 GLY A 508 SER A 509 0 3.15 SITE 1 AC1 4 SER B 339 ILE B 341 ALA B 344 DT P 4 SITE 1 AC2 4 ARG A 386 SER A 417 GLY A 426 HOH A 708 CRYST1 83.693 83.693 396.326 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 0.011948 0.006898 0.000000 0.00000 SCALE2 0.000000 0.013797 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002523 0.00000