HEADER TRANSFERASE/DNA 09-APR-20 6WIE TITLE POST-CATALYTIC NICKED COMPLEX OF HUMAN POLYMERASE MU ON A TITLE 2 COMPLEMENTARY DNA DOUBLE-STRAND BREAK SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 132-494; COMPND 5 SYNONYM: POL MU,TERMINAL TRANSFERASE; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*T)-3'); COMPND 11 CHAIN: T; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*CP*G)-3'); COMPND 15 CHAIN: U; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*T)-3'); COMPND 19 CHAIN: P; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 5; COMPND 22 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 23 CHAIN: D; COMPND 24 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: POLM, POLMU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630; SOURCE 23 MOL_ID: 5; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 26 ORGANISM_TAXID: 32630 KEYWDS FAMILY X POLYMERASE, NONHOMOLOGOUS END-JOINING, DNA DOUBLE-STRAND KEYWDS 2 BREAK REPAIR, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.M.KAMINSKI,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK REVDAT 2 18-OCT-23 6WIE 1 REMARK REVDAT 1 07-OCT-20 6WIE 0 JRNL AUTH A.M.KAMINSKI,J.M.PRYOR,D.A.RAMSDEN,T.A.KUNKEL,L.C.PEDERSEN, JRNL AUTH 2 K.BEBENEK JRNL TITL STRUCTURAL SNAPSHOTS OF HUMAN DNA POLYMERASE MU ENGAGED ON A JRNL TITL 2 DNA DOUBLE-STRAND BREAK. JRNL REF NAT COMMUN V. 11 4784 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32963245 JRNL DOI 10.1038/S41467-020-18506-5 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 71906 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2217 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 34.9000 - 3.7700 0.99 4601 143 0.1681 0.1687 REMARK 3 2 3.7700 - 2.9900 1.00 4442 140 0.1631 0.1719 REMARK 3 3 2.9900 - 2.6200 1.00 4417 134 0.1792 0.2008 REMARK 3 4 2.6200 - 2.3800 1.00 4395 143 0.1732 0.1950 REMARK 3 5 2.3800 - 2.2100 1.00 4358 138 0.1649 0.1928 REMARK 3 6 2.2100 - 2.0800 1.00 4344 139 0.1653 0.1840 REMARK 3 7 2.0800 - 1.9700 1.00 4363 142 0.1684 0.1827 REMARK 3 8 1.9700 - 1.8900 1.00 4323 137 0.1672 0.1836 REMARK 3 9 1.8900 - 1.8100 1.00 4354 132 0.1593 0.2032 REMARK 3 10 1.8100 - 1.7500 1.00 4325 143 0.1651 0.2001 REMARK 3 11 1.7500 - 1.7000 1.00 4308 144 0.1638 0.1826 REMARK 3 12 1.7000 - 1.6500 1.00 4314 133 0.1684 0.1990 REMARK 3 13 1.6500 - 1.6000 1.00 4320 135 0.1739 0.1954 REMARK 3 14 1.6000 - 1.5700 1.00 4315 138 0.1835 0.2195 REMARK 3 15 1.5700 - 1.5300 1.00 4305 153 0.1981 0.2151 REMARK 3 16 1.5300 - 1.5000 0.98 4205 123 0.2249 0.2597 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) : 0.138 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.026 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.57 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 3265 REMARK 3 ANGLE : 1.030 4519 REMARK 3 CHIRALITY : 0.073 489 REMARK 3 PLANARITY : 0.007 527 REMARK 3 DIHEDRAL : 12.979 1029 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 135:231 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0432 -18.1968 -18.1211 REMARK 3 T TENSOR REMARK 3 T11: 0.1120 T22: 0.1151 REMARK 3 T33: 0.1840 T12: 0.0318 REMARK 3 T13: -0.0213 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.7124 L22: 0.7704 REMARK 3 L33: 0.3890 L12: 0.0133 REMARK 3 L13: -0.1644 L23: 0.0382 REMARK 3 S TENSOR REMARK 3 S11: -0.0375 S12: 0.0174 S13: -0.1468 REMARK 3 S21: 0.0387 S22: -0.0138 S23: -0.1763 REMARK 3 S31: 0.0490 S32: 0.0810 S33: -0.0223 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 232:289 REMARK 3 ORIGIN FOR THE GROUP (A): 16.8910 9.5916 -19.1266 REMARK 3 T TENSOR REMARK 3 T11: 0.1655 T22: 0.1681 REMARK 3 T33: 0.1638 T12: -0.0299 REMARK 3 T13: 0.0208 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.0929 L22: 0.4331 REMARK 3 L33: 0.2363 L12: -0.0334 REMARK 3 L13: 0.1994 L23: 0.2512 REMARK 3 S TENSOR REMARK 3 S11: -0.0035 S12: -0.0526 S13: 0.1087 REMARK 3 S21: -0.1327 S22: 0.0369 S23: -0.1764 REMARK 3 S31: -0.2388 S32: 0.2322 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 290:423 REMARK 3 ORIGIN FOR THE GROUP (A): -0.6405 6.7630 -1.1801 REMARK 3 T TENSOR REMARK 3 T11: 0.1298 T22: 0.1229 REMARK 3 T33: 0.1023 T12: -0.0017 REMARK 3 T13: 0.0014 T23: -0.0307 REMARK 3 L TENSOR REMARK 3 L11: 0.6649 L22: 0.6564 REMARK 3 L33: 0.3990 L12: 0.1923 REMARK 3 L13: -0.0232 L23: -0.0284 REMARK 3 S TENSOR REMARK 3 S11: 0.0227 S12: -0.0932 S13: 0.0926 REMARK 3 S21: 0.1624 S22: -0.0069 S23: -0.0027 REMARK 3 S31: -0.0590 S32: -0.0083 S33: 0.0004 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 424:494 REMARK 3 ORIGIN FOR THE GROUP (A): -8.0624 -12.4208 -12.0960 REMARK 3 T TENSOR REMARK 3 T11: 0.0957 T22: 0.1140 REMARK 3 T33: 0.1247 T12: -0.0013 REMARK 3 T13: 0.0025 T23: -0.0294 REMARK 3 L TENSOR REMARK 3 L11: 0.3715 L22: 0.7576 REMARK 3 L33: 0.8496 L12: -0.2368 REMARK 3 L13: -0.0006 L23: 0.2547 REMARK 3 S TENSOR REMARK 3 S11: -0.0001 S12: 0.0227 S13: -0.1671 REMARK 3 S21: 0.0442 S22: -0.0610 S23: 0.1032 REMARK 3 S31: 0.0357 S32: -0.0534 S33: -0.0643 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 2.3961 -15.3099 -30.7164 REMARK 3 T TENSOR REMARK 3 T11: 0.1606 T22: 0.1409 REMARK 3 T33: 0.1173 T12: 0.0144 REMARK 3 T13: -0.0284 T23: -0.0422 REMARK 3 L TENSOR REMARK 3 L11: 0.0341 L22: 0.2297 REMARK 3 L33: 0.1257 L12: 0.1366 REMARK 3 L13: -0.1171 L23: -0.1256 REMARK 3 S TENSOR REMARK 3 S11: 0.0298 S12: -0.0459 S13: -0.0903 REMARK 3 S21: -0.2273 S22: -0.0099 S23: 0.0403 REMARK 3 S31: -0.0604 S32: -0.0459 S33: -0.0014 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN U OR CHAIN P REMARK 3 ORIGIN FOR THE GROUP (A): 0.1089 3.5281 -17.7408 REMARK 3 T TENSOR REMARK 3 T11: 0.1496 T22: 0.1228 REMARK 3 T33: 0.0954 T12: 0.0088 REMARK 3 T13: -0.0048 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.0497 L22: 0.0703 REMARK 3 L33: 0.0620 L12: 0.0291 REMARK 3 L13: 0.0544 L23: 0.0706 REMARK 3 S TENSOR REMARK 3 S11: 0.1544 S12: 0.1192 S13: -0.0593 REMARK 3 S21: 0.0445 S22: -0.1205 S23: 0.0549 REMARK 3 S31: -0.0327 S32: 0.0385 S33: 0.0000 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 6WIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000248268. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.6 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 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) 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 : 71986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10600 REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.57500 REMARK 200 FOR SHELL : 1.770 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: PDB ENTRY 4M04 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40-45.5 MM MES, PH 5.6, 0.16-0.182 M REMARK 280 POTASSIUM CHLORIDE, 8.2-9.1 MM MAGNESIUM SULFATE, 8.2-9.1% W/V REMARK 280 PEG400, VAPOR 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 30.03650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.15900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.12350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.15900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.03650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.12350 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 APPLY THE FOLLOWING TO CHAINS: A, T, U, P, 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 GLY A 127 REMARK 465 SER A 128 REMARK 465 ALA A 129 REMARK 465 ALA A 130 REMARK 465 ALA A 131 REMARK 465 PRO A 132 REMARK 465 LEU A 133 REMARK 465 SER A 134 REMARK 465 GLN A 366 REMARK 465 HIS A 367 REMARK 465 SER A 368 REMARK 465 CYS A 369 REMARK 465 CYS A 370 REMARK 465 GLU A 371 REMARK 465 SER A 372 REMARK 465 PRO A 373 REMARK 465 THR A 374 REMARK 465 ARG A 375 REMARK 465 LEU A 376 REMARK 465 ALA A 377 REMARK 465 GLN A 378 REMARK 465 GLN A 379 REMARK 465 SER A 380 REMARK 465 HIS A 381 REMARK 465 MET A 382 REMARK 465 ASP A 383 REMARK 465 ALA A 384 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 PRO A 135 N CB CG CD REMARK 470 ARG A 175 CZ NH1 NH2 REMARK 470 GLN A 200 CG CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 GLU A 223 CD OE1 OE2 REMARK 470 ARG A 227 CD NE CZ NH1 NH2 REMARK 470 ARG A 230 CD NE CZ NH1 NH2 REMARK 470 LYS A 249 NZ REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 LYS A 271 NZ REMARK 470 GLN A 274 CG CD OE1 NE2 REMARK 470 GLN A 300 CD OE1 NE2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 LYS A 339 CG CD CE NZ REMARK 470 GLN A 355 CG CD OE1 NE2 REMARK 470 GLN A 357 CD OE1 NE2 REMARK 470 GLU A 465 OE1 OE2 REMARK 470 GLN A 466 CG CD OE1 NE2 REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLU A 485 CD OE1 OE2 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' -0.049 REMARK 500 DT P 5 P DT P 5 O5' -0.062 REMARK 500 DG D 1 P DG D 1 OP3 -0.125 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 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT P 3 N3 - C4 - O4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT P 5 O4' - C1' - N1 ANGL. DEV. = 1.9 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 LEU A 310 102.73 -160.68 REMARK 500 THR A 318 -154.09 -124.93 REMARK 500 THR A 318 -149.94 -127.46 REMARK 500 SER A 411 -150.38 -164.62 REMARK 500 ASN A 493 43.75 -86.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE A 509 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 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 96.0 REMARK 620 3 VAL A 246 O 86.6 89.5 REMARK 620 4 HOH A 805 O 86.7 85.5 171.2 REMARK 620 5 DT P 3 OP1 172.5 88.6 87.5 99.6 REMARK 620 6 HOH P 115 O 91.2 170.7 85.0 100.9 83.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 132.0 REMARK 620 3 ASP A 418 OD2 100.5 98.9 REMARK 620 4 DA P 4 O3' 115.4 104.2 99.2 REMARK 620 5 DT P 5 OP1 81.1 98.9 154.2 58.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 330 OD2 44.2 REMARK 620 3 ASP A 332 OD1 90.9 128.8 REMARK 620 4 DA P 4 O3' 127.5 119.7 106.6 REMARK 620 5 DT P 5 OP1 67.0 84.0 101.5 61.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 92.4 REMARK 620 3 SO4 A 506 O4 170.8 94.2 REMARK 620 4 PPV A 507 O11 171.3 93.7 0.6 REMARK 620 5 PPV A 507 O32 75.2 167.2 98.5 99.0 REMARK 620 6 HOH A 629 O 83.7 176.0 89.7 90.2 9.0 REMARK 620 7 HOH A 745 O 82.8 89.4 90.7 91.0 91.7 89.9 REMARK 620 8 DT P 5 OP1 88.9 87.2 97.9 97.7 89.7 93.0 170.9 REMARK 620 N 1 2 3 4 5 6 7 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 511 DBREF 6WIE A 132 494 UNP Q9NP87 DPOLM_HUMAN 132 494 DBREF 6WIE T 1 6 PDB 6WIE 6WIE 1 6 DBREF 6WIE U 1 3 PDB 6WIE 6WIE 1 3 DBREF 6WIE P 1 5 PDB 6WIE 6WIE 1 5 DBREF 6WIE D 1 4 PDB 6WIE 6WIE 1 4 SEQADV 6WIE GLY A 127 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIE SER A 128 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIE ALA A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIE ALA A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIE ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIE A UNP Q9NP87 PRO 398 DELETION SEQADV 6WIE A UNP Q9NP87 GLY 399 DELETION SEQADV 6WIE A UNP Q9NP87 ALA 400 DELETION SEQADV 6WIE A UNP Q9NP87 ALA 401 DELETION SEQADV 6WIE A UNP Q9NP87 VAL 402 DELETION SEQADV 6WIE A UNP Q9NP87 GLY 403 DELETION SEQADV 6WIE A UNP Q9NP87 GLY 404 DELETION SEQADV 6WIE A UNP Q9NP87 SER 405 DELETION SEQADV 6WIE A UNP Q9NP87 THR 406 DELETION SEQADV 6WIE A UNP Q9NP87 ARG 407 DELETION SEQADV 6WIE A UNP Q9NP87 PRO 408 DELETION SEQADV 6WIE A UNP Q9NP87 CYS 409 DELETION SEQADV 6WIE GLY A 410 UNP Q9NP87 PRO 410 LINKER SEQRES 1 A 356 GLY SER ALA ALA ALA PRO LEU SER PRO ALA TRP MET PRO SEQRES 2 A 356 ALA TYR ALA CYS GLN ARG PRO THR PRO LEU THR HIS HIS SEQRES 3 A 356 ASN THR GLY LEU SER GLU ALA LEU GLU ILE LEU ALA GLU SEQRES 4 A 356 ALA ALA GLY PHE GLU GLY SER GLU GLY ARG LEU LEU THR SEQRES 5 A 356 PHE CYS ARG ALA ALA SER VAL LEU LYS ALA LEU PRO SER SEQRES 6 A 356 PRO VAL THR THR LEU SER GLN LEU GLN GLY LEU PRO HIS SEQRES 7 A 356 PHE GLY GLU HIS SER SER ARG VAL VAL GLN GLU LEU LEU SEQRES 8 A 356 GLU HIS GLY VAL CYS GLU GLU VAL GLU ARG VAL ARG ARG SEQRES 9 A 356 SER GLU ARG TYR GLN THR MET LYS LEU PHE THR GLN ILE SEQRES 10 A 356 PHE GLY VAL GLY VAL LYS THR ALA ASP ARG TRP TYR ARG SEQRES 11 A 356 GLU GLY LEU ARG THR LEU ASP ASP LEU ARG GLU GLN PRO SEQRES 12 A 356 GLN LYS LEU THR GLN GLN GLN LYS ALA GLY LEU GLN HIS SEQRES 13 A 356 HIS GLN ASP LEU SER THR PRO VAL LEU ARG SER ASP VAL SEQRES 14 A 356 ASP ALA LEU GLN GLN VAL VAL GLU GLU ALA VAL GLY GLN SEQRES 15 A 356 ALA LEU PRO GLY ALA THR VAL THR LEU THR GLY GLY PHE SEQRES 16 A 356 ARG ARG GLY LYS LEU GLN GLY HIS ASP VAL ASP PHE LEU SEQRES 17 A 356 ILE THR HIS PRO LYS GLU GLY GLN GLU ALA GLY LEU LEU SEQRES 18 A 356 PRO ARG VAL MET CYS ARG LEU GLN ASP GLN GLY LEU ILE SEQRES 19 A 356 LEU TYR HIS GLN HIS GLN HIS SER CYS CYS GLU SER PRO SEQRES 20 A 356 THR ARG LEU ALA GLN GLN SER HIS MET ASP ALA PHE GLU SEQRES 21 A 356 ARG SER PHE CYS ILE PHE ARG LEU PRO GLN PRO GLY SER SEQRES 22 A 356 TRP LYS ALA VAL ARG VAL ASP LEU VAL VAL ALA PRO VAL SEQRES 23 A 356 SER GLN PHE PRO PHE ALA LEU LEU GLY TRP THR GLY SER SEQRES 24 A 356 LYS LEU PHE GLN ARG GLU LEU ARG ARG PHE SER ARG LYS SEQRES 25 A 356 GLU LYS GLY LEU TRP LEU ASN SER HIS GLY LEU PHE ASP SEQRES 26 A 356 PRO GLU GLN LYS THR PHE PHE GLN ALA ALA SER GLU GLU SEQRES 27 A 356 ASP ILE PHE ARG HIS LEU GLY LEU GLU TYR LEU PRO PRO SEQRES 28 A 356 GLU GLN ARG ASN ALA SEQRES 1 T 6 DC DG DG DC DA DT SEQRES 1 U 3 DA DC DG SEQRES 1 P 5 DC DG DT DA DT SEQRES 1 D 4 DG DC DC DG HET MG A 501 1 HET NA A 502 1 HET MG A 503 1 HET NA A 504 1 HET CL A 505 1 HET SO4 A 506 5 HET PPV A 507 9 HET PEG A 508 7 HET 1PE A 509 13 HET PEG A 510 7 HET GOL A 511 6 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM PPV PYROPHOSPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM GOL GLYCEROL HETSYN 1PE PEG400 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 6 MG 2(MG 2+) FORMUL 7 NA 2(NA 1+) FORMUL 10 CL CL 1- FORMUL 11 SO4 O4 S 2- FORMUL 12 PPV H4 O7 P2 FORMUL 13 PEG 2(C4 H10 O3) FORMUL 14 1PE C10 H22 O6 FORMUL 16 GOL C3 H8 O3 FORMUL 17 HOH *347(H2 O) HELIX 1 AA1 TYR A 141 ARG A 145 5 5 HELIX 2 AA2 ASN A 153 GLU A 170 1 18 HELIX 3 AA3 SER A 172 LEU A 189 1 18 HELIX 4 AA4 THR A 195 GLN A 200 5 6 HELIX 5 AA5 GLY A 206 GLY A 220 1 15 HELIX 6 AA6 CYS A 222 SER A 231 1 10 HELIX 7 AA7 SER A 231 GLN A 242 1 12 HELIX 8 AA8 GLY A 247 GLU A 257 1 11 HELIX 9 AA9 THR A 261 GLU A 267 1 7 HELIX 10 AB1 GLN A 268 LEU A 272 5 5 HELIX 11 AB2 THR A 273 HIS A 282 1 10 HELIX 12 AB3 HIS A 282 SER A 287 1 6 HELIX 13 AB4 ARG A 292 LEU A 310 1 19 HELIX 14 AB5 THR A 318 ARG A 323 1 6 HELIX 15 AB6 GLY A 345 GLN A 357 1 13 HELIX 16 AB7 PRO A 423 SER A 425 5 3 HELIX 17 AB8 GLN A 426 GLY A 436 1 11 HELIX 18 AB9 SER A 437 GLY A 453 1 17 HELIX 19 AC1 SER A 474 LEU A 482 1 9 HELIX 20 AC2 PRO A 488 ARG A 492 5 5 SHEET 1 AA1 2 VAL A 290 LEU A 291 0 SHEET 2 AA1 2 GLN A 327 GLY A 328 -1 O GLY A 328 N VAL A 290 SHEET 1 AA2 5 THR A 314 LEU A 317 0 SHEET 2 AA2 5 VAL A 331 THR A 336 -1 O LEU A 334 N THR A 316 SHEET 3 AA2 5 SER A 411 VAL A 421 1 O VAL A 420 N ILE A 335 SHEET 4 AA2 5 ARG A 387 GLN A 396 -1 N PHE A 392 O VAL A 415 SHEET 5 AA2 5 ILE A 360 TYR A 362 -1 N LEU A 361 O ILE A 391 SHEET 1 AA3 3 TRP A 455 ASN A 457 0 SHEET 2 AA3 3 GLY A 460 ASP A 463 -1 O PHE A 462 N TRP A 455 SHEET 3 AA3 3 THR A 468 PHE A 469 -1 O THR A 468 N ASP A 463 LINK O THR A 241 NA NA A 504 1555 1555 2.41 LINK O ILE A 243 NA NA A 504 1555 1555 2.55 LINK O VAL A 246 NA NA A 504 1555 1555 2.40 LINK OD2 ASP A 330 MG A MG A 501 1555 1555 1.94 LINK OD1 ASP A 330 NA B NA A 502 1555 1555 3.09 LINK OD2 ASP A 330 NA B NA A 502 1555 1555 1.95 LINK OD1 ASP A 330 MG MG A 503 1555 1555 2.14 LINK OD1 ASP A 332 MG A MG A 501 1555 1555 1.91 LINK OD1 ASP A 332 NA B NA A 502 1555 1555 1.95 LINK OD2 ASP A 332 MG MG A 503 1555 1555 2.20 LINK OD2 ASP A 418 MG A MG A 501 1555 1555 1.80 LINK MG A MG A 501 O3' DA P 4 1555 1555 2.65 LINK MG A MG A 501 OP1 DT P 5 1555 1555 2.33 LINK NA B NA A 502 O3' DA P 4 1555 1555 2.55 LINK NA B NA A 502 OP1 DT P 5 1555 1555 2.22 LINK MG MG A 503 O4 ASO4 A 506 1555 1555 2.10 LINK MG MG A 503 O11BPPV A 507 1555 1555 2.16 LINK MG MG A 503 O32BPPV A 507 1555 1555 2.02 LINK MG MG A 503 O AHOH A 629 1555 1555 1.87 LINK MG MG A 503 O HOH A 745 1555 1555 2.19 LINK MG MG A 503 OP1 DT P 5 1555 1555 2.17 LINK NA NA A 504 O HOH A 805 1555 1555 2.35 LINK NA NA A 504 OP1 DT P 3 1555 1555 2.75 LINK NA NA A 504 O HOH P 115 1555 1555 2.36 CISPEP 1 GLY A 436 SER A 437 0 -6.24 SITE 1 AC1 6 ASP A 330 ASP A 332 ASP A 418 MG A 503 SITE 2 AC1 6 DA P 4 DT P 5 SITE 1 AC2 6 ASP A 330 ASP A 332 ASP A 418 MG A 503 SITE 2 AC2 6 DA P 4 DT P 5 SITE 1 AC3 9 ASP A 330 ASP A 332 MG A 501 NA A 502 SITE 2 AC3 9 SO4 A 506 PPV A 507 HOH A 629 HOH A 745 SITE 3 AC3 9 DT P 5 SITE 1 AC4 6 THR A 241 ILE A 243 VAL A 246 HOH A 805 SITE 2 AC4 6 DT P 3 HOH P 115 SITE 1 AC5 1 LEU A 326 SITE 1 AC6 12 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC6 12 ASP A 332 MG A 503 PPV A 507 HOH A 611 SITE 3 AC6 12 HOH A 629 HOH A 635 HOH A 745 DT P 5 SITE 1 AC7 16 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC7 16 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC7 16 MG A 503 SO4 A 506 HOH A 611 HOH A 629 SITE 4 AC7 16 HOH A 635 HOH A 654 HOH A 745 DT P 5 SITE 1 AC8 8 HIS A 152 PRO A 192 THR A 314 VAL A 424 SITE 2 AC8 8 PHE A 427 ALA A 473 HOH A 642 HOH A 754 SITE 1 AC9 3 ARG A 253 ARG A 256 GLU A 451 SITE 1 AD1 4 GLN A 426 HIS A 459 HOH A 668 HOH A 838 SITE 1 AD2 8 SER A 425 HIS A 459 GLY A 460 PHE A 469 SITE 2 AD2 8 GLN A 471 HOH A 626 HOH A 637 HOH A 655 CRYST1 60.073 62.247 118.318 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 0.016646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008452 0.00000