HEADER TRANSFERASE/DNA 09-APR-20 6WIC TITLE PRE-CATALYTIC QUATERNARY 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*A)-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 6WIC 1 REMARK REVDAT 1 07-OCT-20 6WIC 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 64729 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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 34.8800 - 3.7300 0.98 4707 149 0.1599 0.1524 REMARK 3 2 3.7300 - 2.9600 0.99 4553 142 0.1658 0.1741 REMARK 3 3 2.9600 - 2.5900 0.99 4529 143 0.1739 0.2068 REMARK 3 4 2.5900 - 2.3500 1.00 4516 144 0.1652 0.1809 REMARK 3 5 2.3500 - 2.1800 1.00 4492 143 0.1575 0.1703 REMARK 3 6 2.1800 - 2.0600 1.00 4482 139 0.1668 0.1899 REMARK 3 7 2.0600 - 1.9500 1.00 4463 147 0.1598 0.1781 REMARK 3 8 1.9500 - 1.8700 0.99 4460 145 0.1595 0.1750 REMARK 3 9 1.8700 - 1.8000 1.00 4450 134 0.1578 0.1853 REMARK 3 10 1.8000 - 1.7300 1.00 4431 148 0.1607 0.2210 REMARK 3 11 1.7300 - 1.6800 1.00 4450 142 0.1681 0.1876 REMARK 3 12 1.6800 - 1.6300 1.00 4427 140 0.1824 0.2248 REMARK 3 13 1.6300 - 1.5900 1.00 4424 142 0.1862 0.1861 REMARK 3 14 1.5900 - 1.5500 0.98 4350 137 0.2181 0.2574 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) : 0.151 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.453 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.42 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 3237 REMARK 3 ANGLE : 1.038 4480 REMARK 3 CHIRALITY : 0.060 488 REMARK 3 PLANARITY : 0.007 520 REMARK 3 DIHEDRAL : 12.745 1021 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): 15.4219 -18.1862 -17.9681 REMARK 3 T TENSOR REMARK 3 T11: 0.1557 T22: 0.1685 REMARK 3 T33: 0.2437 T12: 0.0343 REMARK 3 T13: -0.0290 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.9380 L22: 0.9834 REMARK 3 L33: 0.4834 L12: 0.0635 REMARK 3 L13: -0.3747 L23: 0.0601 REMARK 3 S TENSOR REMARK 3 S11: -0.0474 S12: -0.0031 S13: -0.1866 REMARK 3 S21: 0.0378 S22: -0.0343 S23: -0.2057 REMARK 3 S31: 0.0680 S32: 0.1124 S33: -0.0499 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 232:289 REMARK 3 ORIGIN FOR THE GROUP (A): 16.8364 9.3724 -18.9437 REMARK 3 T TENSOR REMARK 3 T11: 0.1987 T22: 0.2085 REMARK 3 T33: 0.2132 T12: -0.0289 REMARK 3 T13: 0.0191 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.0084 L22: 0.4473 REMARK 3 L33: 0.2391 L12: -0.2085 REMARK 3 L13: 0.0575 L23: 0.3536 REMARK 3 S TENSOR REMARK 3 S11: 0.0492 S12: -0.0486 S13: 0.1210 REMARK 3 S21: -0.0968 S22: -0.0017 S23: -0.2077 REMARK 3 S31: -0.1920 S32: 0.1951 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 290:423 REMARK 3 ORIGIN FOR THE GROUP (A): -0.6054 6.7172 -1.1115 REMARK 3 T TENSOR REMARK 3 T11: 0.1855 T22: 0.1638 REMARK 3 T33: 0.1303 T12: -0.0055 REMARK 3 T13: 0.0039 T23: -0.0312 REMARK 3 L TENSOR REMARK 3 L11: 0.7691 L22: 0.7528 REMARK 3 L33: 0.3930 L12: 0.1223 REMARK 3 L13: -0.0479 L23: 0.0792 REMARK 3 S TENSOR REMARK 3 S11: 0.0381 S12: -0.1236 S13: 0.0937 REMARK 3 S21: 0.1929 S22: -0.0181 S23: -0.0078 REMARK 3 S31: -0.0852 S32: 0.0001 S33: -0.0042 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 424:494 REMARK 3 ORIGIN FOR THE GROUP (A): -8.2913 -12.3155 -12.4472 REMARK 3 T TENSOR REMARK 3 T11: 0.1308 T22: 0.1483 REMARK 3 T33: 0.1790 T12: 0.0001 REMARK 3 T13: 0.0013 T23: -0.0391 REMARK 3 L TENSOR REMARK 3 L11: 0.7431 L22: 0.9706 REMARK 3 L33: 1.0227 L12: -0.5309 REMARK 3 L13: -0.1580 L23: 0.2244 REMARK 3 S TENSOR REMARK 3 S11: 0.0155 S12: 0.0579 S13: -0.2328 REMARK 3 S21: 0.0469 S22: -0.1027 S23: 0.1507 REMARK 3 S31: 0.0065 S32: -0.0601 S33: -0.0600 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 2.4497 -15.2454 -30.6640 REMARK 3 T TENSOR REMARK 3 T11: 0.1957 T22: 0.1908 REMARK 3 T33: 0.1629 T12: 0.0126 REMARK 3 T13: -0.0348 T23: -0.0512 REMARK 3 L TENSOR REMARK 3 L11: -0.0226 L22: 0.3836 REMARK 3 L33: 0.1829 L12: 0.2005 REMARK 3 L13: -0.1752 L23: -0.0419 REMARK 3 S TENSOR REMARK 3 S11: -0.0207 S12: -0.0220 S13: -0.0767 REMARK 3 S21: -0.1940 S22: 0.0500 S23: 0.0446 REMARK 3 S31: 0.0061 S32: -0.0952 S33: 0.0007 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN U OR CHAIN P REMARK 3 ORIGIN FOR THE GROUP (A): -0.3499 4.5358 -18.6465 REMARK 3 T TENSOR REMARK 3 T11: 0.1860 T22: 0.1731 REMARK 3 T33: 0.1340 T12: 0.0188 REMARK 3 T13: -0.0021 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.0652 L22: 0.1131 REMARK 3 L33: 0.1152 L12: 0.0282 REMARK 3 L13: -0.0205 L23: 0.0844 REMARK 3 S TENSOR REMARK 3 S11: 0.0504 S12: 0.0347 S13: -0.0873 REMARK 3 S21: 0.0563 S22: -0.0644 S23: -0.0152 REMARK 3 S31: 0.0127 S32: 0.0247 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 6WIC 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_1000248264. 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 : 64813 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 26.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53500 REMARK 200 FOR SHELL : 1.500 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 (%): 49.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 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 30.06700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.02700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.11650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.02700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.06700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.11650 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: 6710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL 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 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 ARG A 211 CD NE CZ NH1 NH2 REMARK 470 GLU A 223 CD OE1 OE2 REMARK 470 ARG A 229 NH1 NH2 REMARK 470 LYS A 249 NZ REMARK 470 GLU A 267 CD OE1 OE2 REMARK 470 GLN A 268 OE1 NE2 REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 LYS A 271 CE 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 GLN A 327 CD OE1 NE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 CG CD OE1 NE2 REMARK 470 GLN A 357 CG CD OE1 NE2 REMARK 470 ARG A 449 CZ NH1 NH2 REMARK 470 LYS A 452 CE NZ REMARK 470 GLN A 466 CD OE1 NE2 REMARK 470 LYS A 467 CE NZ REMARK 470 GLU A 485 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 O HOH A 857 O HOH A 1033 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 DT P 3 O3' DT P 3 C3' -0.044 REMARK 500 DG D 1 P DG D 1 OP3 -0.124 REMARK 500 DC D 3 O3' DC D 3 C3' -0.038 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. = -3.6 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 2.1 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 SER A 172 78.06 -106.23 REMARK 500 LEU A 310 104.58 -160.67 REMARK 500 THR A 318 -146.23 -124.86 REMARK 500 THR A 318 -156.90 -130.91 REMARK 500 SER A 411 -150.21 -165.90 REMARK 500 ASN A 493 45.74 -86.94 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 709 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 704 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 94.7 REMARK 620 3 VAL A 246 O 83.0 89.3 REMARK 620 4 HOH A1026 O 87.9 88.1 170.3 REMARK 620 5 DT P 3 OP1 169.3 91.1 88.1 101.3 REMARK 620 6 HOH P 115 O 89.7 167.4 79.6 103.8 82.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 705 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 93.0 REMARK 620 3 VAL A 246 O 82.9 86.3 REMARK 620 4 HOH A1026 O 89.4 86.7 169.3 REMARK 620 5 DT P 3 OP1 169.3 88.3 86.6 101.3 REMARK 620 6 HOH P 115 O 92.6 164.9 80.5 107.4 83.7 REMARK 620 7 HOH P 117 O 136.3 94.4 140.5 48.3 54.0 91.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 93.9 REMARK 620 3 DUP A 701 O2A 96.9 89.4 REMARK 620 4 DUP A 701 O2B 172.1 91.3 89.2 REMARK 620 5 DUP A 701 O1G 86.2 178.9 91.7 88.5 REMARK 620 6 HOH A 917 O 84.6 87.2 176.4 89.7 91.7 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 330 OD2 REMARK 620 2 ASP A 332 OD1 101.3 REMARK 620 3 ASP A 418 OD2 86.7 96.2 REMARK 620 4 DUP A 701 O2A 95.1 90.5 172.6 REMARK 620 5 DA P 4 O3' 169.0 84.4 83.3 94.3 REMARK 620 6 HOH P 103 O 86.7 170.1 90.0 82.9 88.8 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 DUP A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 709 DBREF 6WIC A 132 494 UNP Q9NP87 DPOLM_HUMAN 132 494 DBREF 6WIC T 1 6 PDB 6WIC 6WIC 1 6 DBREF 6WIC U 1 3 PDB 6WIC 6WIC 1 3 DBREF 6WIC P 1 4 PDB 6WIC 6WIC 1 4 DBREF 6WIC D 1 4 PDB 6WIC 6WIC 1 4 SEQADV 6WIC GLY A 127 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIC SER A 128 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIC ALA A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIC ALA A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIC ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6WIC A UNP Q9NP87 PRO 398 DELETION SEQADV 6WIC A UNP Q9NP87 GLY 399 DELETION SEQADV 6WIC A UNP Q9NP87 ALA 400 DELETION SEQADV 6WIC A UNP Q9NP87 ALA 401 DELETION SEQADV 6WIC A UNP Q9NP87 VAL 402 DELETION SEQADV 6WIC A UNP Q9NP87 GLY 403 DELETION SEQADV 6WIC A UNP Q9NP87 GLY 404 DELETION SEQADV 6WIC A UNP Q9NP87 SER 405 DELETION SEQADV 6WIC A UNP Q9NP87 THR 406 DELETION SEQADV 6WIC A UNP Q9NP87 ARG 407 DELETION SEQADV 6WIC A UNP Q9NP87 PRO 408 DELETION SEQADV 6WIC A UNP Q9NP87 CYS 409 DELETION SEQADV 6WIC 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 4 DC DG DT DA SEQRES 1 D 4 DG DC DC DG HET DUP A 701 28 HET MG A 702 1 HET MG A 703 1 HET NA A 704 1 HET K A 705 1 HET CL A 706 1 HET GOL A 707 6 HET PEG A 708 7 HET 1PE A 709 13 HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 1PE PEG400 FORMUL 6 DUP C9 H16 N3 O13 P3 FORMUL 7 MG 2(MG 2+) FORMUL 9 NA NA 1+ FORMUL 10 K K 1+ FORMUL 11 CL CL 1- FORMUL 12 GOL C3 H8 O3 FORMUL 13 PEG C4 H10 O3 FORMUL 14 1PE C10 H22 O6 FORMUL 15 HOH *349(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 A NA A 704 1555 1555 2.55 LINK O THR A 241 K B K A 705 1555 1555 2.51 LINK O ILE A 243 NA A NA A 704 1555 1555 2.58 LINK O ILE A 243 K B K A 705 1555 1555 2.68 LINK O VAL A 246 NA A NA A 704 1555 1555 2.51 LINK O VAL A 246 K B K A 705 1555 1555 2.55 LINK OD1 ASP A 330 MG MG A 702 1555 1555 2.03 LINK OD2 ASP A 330 MG MG A 703 1555 1555 2.01 LINK OD2 ASP A 332 MG MG A 702 1555 1555 2.05 LINK OD1 ASP A 332 MG MG A 703 1555 1555 2.04 LINK OD2 ASP A 418 MG MG A 703 1555 1555 2.01 LINK O2A DUP A 701 MG MG A 702 1555 1555 2.13 LINK O2B DUP A 701 MG MG A 702 1555 1555 2.07 LINK O1G DUP A 701 MG MG A 702 1555 1555 2.08 LINK O2A DUP A 701 MG MG A 703 1555 1555 2.23 LINK MG MG A 702 O HOH A 917 1555 1555 2.20 LINK MG MG A 703 O3' DA P 4 1555 1555 2.23 LINK MG MG A 703 O HOH P 103 1555 1555 2.08 LINK NA A NA A 704 O HOH A1026 1555 1555 2.60 LINK NA A NA A 704 OP1 DT P 3 1555 1555 2.75 LINK NA A NA A 704 O HOH P 115 1555 1555 2.58 LINK K B K A 705 O HOH A1026 1555 1555 2.57 LINK K B K A 705 OP1 DT P 3 1555 1555 2.78 LINK K B K A 705 O HOH P 115 1555 1555 2.49 LINK K B K A 705 O HOH P 117 1555 1555 3.44 CISPEP 1 GLY A 436 SER A 437 0 -7.61 SITE 1 AC1 29 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC1 29 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC1 29 GLY A 433 TRP A 434 GLY A 436 LYS A 438 SITE 4 AC1 29 MG A 702 MG A 703 HOH A 870 HOH A 889 SITE 5 AC1 29 HOH A 912 HOH A 917 HOH A 924 HOH A 934 SITE 6 AC1 29 HOH A 935 HOH A 949 HOH A 954 HOH A 965 SITE 7 AC1 29 HOH A 998 HOH A1025 DA P 4 HOH P 103 SITE 8 AC1 29 DA T 5 SITE 1 AC2 5 ASP A 330 ASP A 332 DUP A 701 MG A 703 SITE 2 AC2 5 HOH A 917 SITE 1 AC3 7 ASP A 330 ASP A 332 ASP A 418 DUP A 701 SITE 2 AC3 7 MG A 702 DA P 4 HOH P 103 SITE 1 AC4 6 THR A 241 ILE A 243 VAL A 246 HOH A1026 SITE 2 AC4 6 DT P 3 HOH P 115 SITE 1 AC5 6 THR A 241 ILE A 243 VAL A 246 HOH A1026 SITE 2 AC5 6 DT P 3 HOH P 115 SITE 1 AC6 5 ARG A 387 ARG A 445 SER A 458 DT T 6 SITE 2 AC6 5 DA U 1 SITE 1 AC7 9 SER A 425 GLN A 426 HIS A 459 GLY A 460 SITE 2 AC7 9 PHE A 469 GLN A 471 HOH A 802 HOH A 865 SITE 3 AC7 9 HOH A 866 SITE 1 AC8 3 GLN A 426 HIS A 459 HOH A 832 SITE 1 AC9 3 ARG A 253 ARG A 256 GLU A 451 CRYST1 60.134 62.233 118.054 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 0.016630 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016069 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008471 0.00000