HEADER TRANSFERASE 20-MAY-19 6P1T TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH 1-NT TITLE 2 GAPPED SUBSTRATE CONTAINING TEMPLATE 8OG AND BOUND CMPCPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL MU,TERMINAL TRANSFERASE; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*CP*GP*TP*A)-3'); COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 17 CHAIN: D; COMPND 18 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: 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: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606 KEYWDS FAMILY X POLYMERASE, NHEJ, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.KAMINSKI,L.C.PEDERSEN,K.BEBENEK,K.K.CHIRUVELLA,D.A.RAMSDEN, AUTHOR 2 T.A.KUNKEL REVDAT 4 11-OCT-23 6P1T 1 LINK REVDAT 3 18-DEC-19 6P1T 1 REMARK REVDAT 2 09-OCT-19 6P1T 1 JRNL REVDAT 1 04-SEP-19 6P1T 0 JRNL AUTH A.M.KAMINSKI,K.K.CHIRUVELLA,D.A.RAMSDEN,T.A.KUNKEL, JRNL AUTH 2 K.BEBENEK,L.C.PEDERSEN JRNL TITL UNEXPECTED BEHAVIOR OF DNA POLYMERASE MU OPPOSITE TEMPLATE JRNL TITL 2 8-OXO-7,8-DIHYDRO-2'-GUANOSINE. JRNL REF NUCLEIC ACIDS RES. V. 47 9410 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 31435651 JRNL DOI 10.1093/NAR/GKZ680 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 49594 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) : 0.169 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2479 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 43.0561 - 4.4524 1.00 2888 152 0.1714 0.2015 REMARK 3 2 4.4524 - 3.5346 1.00 2746 146 0.1410 0.1415 REMARK 3 3 3.5346 - 3.0879 1.00 2735 144 0.1604 0.1725 REMARK 3 4 3.0879 - 2.8056 1.00 2688 140 0.1853 0.2113 REMARK 3 5 2.8056 - 2.6046 1.00 2678 140 0.1841 0.2082 REMARK 3 6 2.6046 - 2.4510 1.00 2697 145 0.1788 0.1847 REMARK 3 7 2.4510 - 2.3283 1.00 2678 139 0.1611 0.1892 REMARK 3 8 2.3283 - 2.2269 1.00 2669 137 0.1610 0.2029 REMARK 3 9 2.2269 - 2.1412 1.00 2665 143 0.1587 0.1868 REMARK 3 10 2.1412 - 2.0673 1.00 2657 140 0.1637 0.1724 REMARK 3 11 2.0673 - 2.0027 1.00 2644 143 0.1724 0.2016 REMARK 3 12 2.0027 - 1.9454 0.99 2650 140 0.1744 0.2026 REMARK 3 13 1.9454 - 1.8942 0.99 2637 135 0.1780 0.2183 REMARK 3 14 1.8942 - 1.8480 0.98 2591 136 0.1821 0.2251 REMARK 3 15 1.8480 - 1.8060 0.98 2577 137 0.1875 0.2354 REMARK 3 16 1.8060 - 1.7676 0.97 2557 135 0.1982 0.2142 REMARK 3 17 1.7676 - 1.7322 0.88 2336 123 0.2312 0.2492 REMARK 3 18 1.7322 - 1.6995 0.77 2022 104 0.2517 0.2981 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.380 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 3164 REMARK 3 ANGLE : 1.087 4389 REMARK 3 CHIRALITY : 0.062 482 REMARK 3 PLANARITY : 0.007 514 REMARK 3 DIHEDRAL : 12.566 1025 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 138:231 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7983 -18.6955 -14.8051 REMARK 3 T TENSOR REMARK 3 T11: 0.1982 T22: 0.1941 REMARK 3 T33: 0.1986 T12: 0.0400 REMARK 3 T13: -0.0092 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 1.3081 L22: 1.3399 REMARK 3 L33: 1.5035 L12: -0.3992 REMARK 3 L13: 0.0170 L23: -0.3745 REMARK 3 S TENSOR REMARK 3 S11: 0.0107 S12: 0.1495 S13: -0.1490 REMARK 3 S21: -0.0836 S22: -0.0944 S23: -0.1373 REMARK 3 S31: 0.1846 S32: 0.2411 S33: 0.0691 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 232:289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.0154 8.0729 -16.7823 REMARK 3 T TENSOR REMARK 3 T11: 0.2206 T22: 0.2333 REMARK 3 T33: 0.2876 T12: -0.0025 REMARK 3 T13: 0.0604 T23: 0.0420 REMARK 3 L TENSOR REMARK 3 L11: 1.1935 L22: 1.1855 REMARK 3 L33: 1.6730 L12: -0.1456 REMARK 3 L13: -0.4079 L23: 0.9038 REMARK 3 S TENSOR REMARK 3 S11: 0.1205 S12: 0.1498 S13: 0.2311 REMARK 3 S21: -0.2529 S22: 0.0098 S23: -0.3237 REMARK 3 S31: -0.2415 S32: 0.1415 S33: -0.1026 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 290:423 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1654 8.7043 -0.4904 REMARK 3 T TENSOR REMARK 3 T11: 0.1709 T22: 0.1592 REMARK 3 T33: 0.1675 T12: -0.0047 REMARK 3 T13: 0.0134 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 2.1337 L22: 1.6166 REMARK 3 L33: 0.4552 L12: -0.3444 REMARK 3 L13: -0.0707 L23: 0.1265 REMARK 3 S TENSOR REMARK 3 S11: 0.0623 S12: -0.1404 S13: 0.3124 REMARK 3 S21: 0.1251 S22: -0.0404 S23: -0.0626 REMARK 3 S31: -0.0867 S32: -0.0276 S33: -0.0141 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 424:494 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.8066 -10.3257 -11.1250 REMARK 3 T TENSOR REMARK 3 T11: 0.1463 T22: 0.1689 REMARK 3 T33: 0.1489 T12: -0.0122 REMARK 3 T13: -0.0108 T23: -0.0183 REMARK 3 L TENSOR REMARK 3 L11: 1.4604 L22: 1.5861 REMARK 3 L33: 1.5857 L12: -0.2215 REMARK 3 L13: -0.2930 L23: 0.1490 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: 0.2362 S13: -0.0924 REMARK 3 S21: -0.0704 S22: -0.0264 S23: 0.1746 REMARK 3 S31: 0.0348 S32: -0.1917 S33: 0.0087 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN P AND RESID 1:4 ) OR ( CHAIN T AND RESID 1:9 REMARK 3 ) OR ( CHAIN D AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.2239 -7.1025 -23.0876 REMARK 3 T TENSOR REMARK 3 T11: 0.2324 T22: 0.2738 REMARK 3 T33: 0.1578 T12: 0.0006 REMARK 3 T13: -0.0100 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: -0.0853 L22: 1.2914 REMARK 3 L33: 0.4859 L12: -0.1056 REMARK 3 L13: 0.1076 L23: 0.3279 REMARK 3 S TENSOR REMARK 3 S11: 0.0992 S12: 0.2180 S13: -0.0235 REMARK 3 S21: -0.2065 S22: -0.1266 S23: 0.0949 REMARK 3 S31: 0.0608 S32: -0.1516 S33: 0.0315 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 6P1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49662 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 97.6 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 31.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54200 REMARK 200 FOR SHELL : 2.090 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: 4M04 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 94MM HEPES PH 7.5, 94MM NACL, 9.4% W/V REMARK 280 PEG4000, 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 29.90250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.21700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.35750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.21700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.90250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.35750 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, 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 129 REMARK 465 SER A 130 REMARK 465 ALA A 131 REMARK 465 ALA A 132 REMARK 465 ALA A 133 REMARK 465 SER A 134 REMARK 465 PRO A 135 REMARK 465 ALA A 136 REMARK 465 TRP A 137 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 GLU A 158 CD OE1 OE2 REMARK 470 GLU A 173 CD OE1 OE2 REMARK 470 GLN A 200 CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 GLU A 267 CD OE1 OE2 REMARK 470 GLN A 268 CG CD OE1 NE2 REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLN A 274 CG CD OE1 NE2 REMARK 470 ASP A 296 CG OD1 OD2 REMARK 470 GLN A 300 CD OE1 NE2 REMARK 470 GLU A 304 OE1 OE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 OE1 NE2 REMARK 470 HIS A 363 ND1 CD2 CE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 GLU A 465 CD OE1 OE2 REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLN A 471 OE1 NE2 REMARK 470 GLU A 485 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 145 O HOH A 601 2.16 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' -0.050 REMARK 500 DG D 1 P DG D 1 OP3 -0.121 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 153 41.20 -141.37 REMARK 500 GLN A 268 62.23 -117.57 REMARK 500 LEU A 310 93.00 -162.34 REMARK 500 THR A 318 -147.94 -122.34 REMARK 500 THR A 318 -155.24 -128.88 REMARK 500 SER A 411 -146.32 -166.15 REMARK 500 ASN A 493 49.59 -86.84 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 EPE A 508 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 97.4 REMARK 620 3 VAL A 246 O 88.2 92.5 REMARK 620 4 HOH A 830 O 90.0 90.4 176.8 REMARK 620 5 DT P 3 OP1 171.1 91.4 92.7 88.7 REMARK 620 6 HOH P 107 O 88.1 172.8 83.1 94.2 83.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 98.8 REMARK 620 3 ASP A 418 OD2 87.1 93.4 REMARK 620 4 2TM A 501 O2A 95.9 92.8 172.6 REMARK 620 5 HOH A 626 O 89.6 170.9 90.4 83.0 REMARK 620 6 DA P 4 O3' 168.5 87.6 82.9 93.3 84.6 REMARK 620 N 1 2 3 4 5 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 93.2 REMARK 620 3 2TM A 501 O2G 85.4 178.4 REMARK 620 4 2TM A 501 O2B 170.4 94.1 87.3 REMARK 620 5 2TM A 501 O2A 95.4 88.4 92.3 91.0 REMARK 620 6 HOH A 705 O 83.7 87.1 92.1 90.4 175.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA T 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT T 6 OP2 REMARK 620 2 DT T 6 O5' 49.2 REMARK 620 3 HOH T 233 O 116.9 101.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2TM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG 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 CL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA T 101 DBREF 6P1T A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 6P1T T 1 9 PDB 6P1T 6P1T 1 9 DBREF 6P1T P 1 4 PDB 6P1T 6P1T 1 4 DBREF 6P1T D 1 4 PDB 6P1T 6P1T 1 4 SEQADV 6P1T GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1T SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1T ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1T ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1T ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1T A UNP Q9NP87 PRO 398 DELETION SEQADV 6P1T A UNP Q9NP87 GLY 399 DELETION SEQADV 6P1T A UNP Q9NP87 ALA 400 DELETION SEQADV 6P1T A UNP Q9NP87 ALA 401 DELETION SEQADV 6P1T A UNP Q9NP87 VAL 402 DELETION SEQADV 6P1T A UNP Q9NP87 GLY 403 DELETION SEQADV 6P1T A UNP Q9NP87 GLY 404 DELETION SEQADV 6P1T A UNP Q9NP87 SER 405 DELETION SEQADV 6P1T A UNP Q9NP87 THR 406 DELETION SEQADV 6P1T A UNP Q9NP87 ARG 407 DELETION SEQADV 6P1T A UNP Q9NP87 PRO 408 DELETION SEQADV 6P1T A UNP Q9NP87 CYS 409 DELETION SEQADV 6P1T GLY A 410 UNP Q9NP87 PRO 410 LINKER SEQRES 1 A 354 GLY SER ALA ALA ALA SER PRO ALA TRP MET PRO ALA TYR SEQRES 2 A 354 ALA CYS GLN ARG PRO THR PRO LEU THR HIS HIS ASN THR SEQRES 3 A 354 GLY LEU SER GLU ALA LEU GLU ILE LEU ALA GLU ALA ALA SEQRES 4 A 354 GLY PHE GLU GLY SER GLU GLY ARG LEU LEU THR PHE CYS SEQRES 5 A 354 ARG ALA ALA SER VAL LEU LYS ALA LEU PRO SER PRO VAL SEQRES 6 A 354 THR THR LEU SER GLN LEU GLN GLY LEU PRO HIS PHE GLY SEQRES 7 A 354 GLU HIS SER SER ARG VAL VAL GLN GLU LEU LEU GLU HIS SEQRES 8 A 354 GLY VAL CYS GLU GLU VAL GLU ARG VAL ARG ARG SER GLU SEQRES 9 A 354 ARG TYR GLN THR MET LYS LEU PHE THR GLN ILE PHE GLY SEQRES 10 A 354 VAL GLY VAL LYS THR ALA ASP ARG TRP TYR ARG GLU GLY SEQRES 11 A 354 LEU ARG THR LEU ASP ASP LEU ARG GLU GLN PRO GLN LYS SEQRES 12 A 354 LEU THR GLN GLN GLN LYS ALA GLY LEU GLN HIS HIS GLN SEQRES 13 A 354 ASP LEU SER THR PRO VAL LEU ARG SER ASP VAL ASP ALA SEQRES 14 A 354 LEU GLN GLN VAL VAL GLU GLU ALA VAL GLY GLN ALA LEU SEQRES 15 A 354 PRO GLY ALA THR VAL THR LEU THR GLY GLY PHE ARG ARG SEQRES 16 A 354 GLY LYS LEU GLN GLY HIS ASP VAL ASP PHE LEU ILE THR SEQRES 17 A 354 HIS PRO LYS GLU GLY GLN GLU ALA GLY LEU LEU PRO ARG SEQRES 18 A 354 VAL MET CYS ARG LEU GLN ASP GLN GLY LEU ILE LEU TYR SEQRES 19 A 354 HIS GLN HIS GLN HIS SER CYS CYS GLU SER PRO THR ARG SEQRES 20 A 354 LEU ALA GLN GLN SER HIS MET ASP ALA PHE GLU ARG SER SEQRES 21 A 354 PHE CYS ILE PHE ARG LEU PRO GLN PRO GLY SER TRP LYS SEQRES 22 A 354 ALA VAL ARG VAL ASP LEU VAL VAL ALA PRO VAL SER GLN SEQRES 23 A 354 PHE PRO PHE ALA LEU LEU GLY TRP THR GLY SER LYS LEU SEQRES 24 A 354 PHE GLN ARG GLU LEU ARG ARG PHE SER ARG LYS GLU LYS SEQRES 25 A 354 GLY LEU TRP LEU ASN SER HIS GLY LEU PHE ASP PRO GLU SEQRES 26 A 354 GLN LYS THR PHE PHE GLN ALA ALA SER GLU GLU ASP ILE SEQRES 27 A 354 PHE ARG HIS LEU GLY LEU GLU TYR LEU PRO PRO GLU GLN SEQRES 28 A 354 ARG ASN ALA SEQRES 1 T 9 DC DG DG DC 8OG DT DA DC DG SEQRES 1 P 4 DC DG DT DA SEQRES 1 D 4 DG DC DC DG HET 8OG T 5 23 HET 2TM A 501 29 HET MG A 502 1 HET MG A 503 1 HET NA A 504 1 HET CL A 505 1 HET CL A 506 1 HET CL A 507 1 HET EPE A 508 5 HET EDO A 509 4 HET EDO A 510 4 HET NA T 101 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 2TM 5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 2TM PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN 2TM CMPCPP HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 5 2TM C10 H18 N3 O13 P3 FORMUL 6 MG 2(MG 2+) FORMUL 8 NA 2(NA 1+) FORMUL 9 CL 3(CL 1-) FORMUL 12 EPE C8 H18 N2 O4 S FORMUL 13 EDO 2(C2 H6 O2) FORMUL 16 HOH *350(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 GLN A 268 1 8 HELIX 10 AB1 PRO A 269 LEU A 272 5 4 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 O3' DC T 4 P 8OG T 5 1555 1555 1.60 LINK O3' 8OG T 5 P DT T 6 1555 1555 1.61 LINK O THR A 241 NA NA A 504 1555 1555 2.44 LINK O ILE A 243 NA NA A 504 1555 1555 2.43 LINK O VAL A 246 NA NA A 504 1555 1555 2.30 LINK OD2 ASP A 330 MG MG A 502 1555 1555 1.99 LINK OD1 ASP A 330 MG MG A 503 1555 1555 2.04 LINK OD1 ASP A 332 MG MG A 502 1555 1555 2.02 LINK OD2 ASP A 332 MG MG A 503 1555 1555 2.04 LINK OD2 ASP A 418 MG MG A 502 1555 1555 2.06 LINK O2A 2TM A 501 MG MG A 502 1555 1555 2.15 LINK O2G 2TM A 501 MG MG A 503 1555 1555 2.10 LINK O2B 2TM A 501 MG MG A 503 1555 1555 2.05 LINK O2A 2TM A 501 MG MG A 503 1555 1555 2.18 LINK MG MG A 502 O HOH A 626 1555 1555 2.08 LINK MG MG A 502 O3' DA P 4 1555 1555 2.15 LINK MG MG A 503 O HOH A 705 1555 1555 2.16 LINK NA NA A 504 O AHOH A 830 1555 1555 2.35 LINK NA NA A 504 OP1 DT P 3 1555 1555 2.66 LINK NA NA A 504 O HOH P 107 1555 1555 2.47 LINK OP2 DT T 6 NA NA T 101 1555 1555 2.35 LINK O5' DT T 6 NA NA T 101 1555 1555 3.19 LINK NA NA T 101 O HOH T 233 1555 1555 2.29 CISPEP 1 GLY A 436 SER A 437 0 -4.35 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 THR A 435 GLY A 436 SITE 4 AC1 29 LYS A 438 GLN A 441 MG A 502 MG A 503 SITE 5 AC1 29 EDO A 509 HOH A 616 HOH A 626 HOH A 641 SITE 6 AC1 29 HOH A 646 HOH A 672 HOH A 698 HOH A 704 SITE 7 AC1 29 HOH A 705 HOH A 753 HOH A 802 DA P 4 SITE 8 AC1 29 8OG T 5 SITE 1 AC2 7 ASP A 330 ASP A 332 ASP A 418 2TM A 501 SITE 2 AC2 7 MG A 503 HOH A 626 DA P 4 SITE 1 AC3 5 ASP A 330 ASP A 332 2TM A 501 MG A 502 SITE 2 AC3 5 HOH A 705 SITE 1 AC4 6 THR A 241 ILE A 243 VAL A 246 HOH A 830 SITE 2 AC4 6 DT P 3 HOH P 107 SITE 1 AC5 3 ARG A 445 SER A 458 DA T 7 SITE 1 AC6 4 SER A 172 GLY A 174 ARG A 175 HOH A 776 SITE 1 AC7 4 SER A 474 GLU A 475 HOH A 810 HOH A 881 SITE 1 AC8 4 LYS A 325 LEU A 326 GLN A 327 HOH A 661 SITE 1 AC9 7 ARG A 387 TRP A 434 ARG A 445 SER A 458 SITE 2 AC9 7 2TM A 501 HOH A 616 DA P 4 SITE 1 AD1 6 SER A 425 PHE A 429 HIS A 459 GLY A 460 SITE 2 AD1 6 GLN A 471 HOH A 695 SITE 1 AD2 2 DT T 6 HOH T 233 CRYST1 59.805 68.715 110.434 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 0.016721 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009055 0.00000