HEADER TRANSFERASE 20-MAY-19 6P1R TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH 1-NT TITLE 2 GAPPED SUBSTRATE CONTAINING TEMPLATE 8OG AND BOUND INCOMING AMPNPP 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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 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 6P1R 1 LINK REVDAT 3 18-DEC-19 6P1R 1 REMARK REVDAT 2 09-OCT-19 6P1R 1 JRNL REVDAT 1 04-SEP-19 6P1R 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) : 31.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 50757 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2537 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 31.3775 - 4.4535 1.00 2885 151 0.1728 0.2116 REMARK 3 2 4.4535 - 3.5364 1.00 2748 146 0.1467 0.1395 REMARK 3 3 3.5364 - 3.0899 1.00 2733 145 0.1662 0.1854 REMARK 3 4 3.0899 - 2.8075 1.00 2695 139 0.1937 0.2010 REMARK 3 5 2.8075 - 2.6064 1.00 2678 140 0.1945 0.2170 REMARK 3 6 2.6064 - 2.4528 1.00 2699 145 0.1828 0.1833 REMARK 3 7 2.4528 - 2.3300 1.00 2673 140 0.1760 0.2090 REMARK 3 8 2.3300 - 2.2286 1.00 2674 136 0.1748 0.2235 REMARK 3 9 2.2286 - 2.1428 1.00 2663 144 0.1712 0.2029 REMARK 3 10 2.1428 - 2.0689 1.00 2655 140 0.1735 0.1904 REMARK 3 11 2.0689 - 2.0042 1.00 2661 143 0.1753 0.2145 REMARK 3 12 2.0042 - 1.9470 1.00 2659 141 0.1776 0.2011 REMARK 3 13 1.9470 - 1.8957 1.00 2674 137 0.1797 0.2192 REMARK 3 14 1.8957 - 1.8495 1.00 2636 139 0.1790 0.1869 REMARK 3 15 1.8495 - 1.8074 1.00 2642 139 0.1865 0.1955 REMARK 3 16 1.8074 - 1.7690 1.00 2637 139 0.2022 0.2204 REMARK 3 17 1.7690 - 1.7336 0.99 2642 140 0.2114 0.2309 REMARK 3 18 1.7336 - 1.7009 0.97 2566 133 0.2348 0.2848 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.190 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 3206 REMARK 3 ANGLE : 1.101 4458 REMARK 3 CHIRALITY : 0.058 485 REMARK 3 PLANARITY : 0.007 521 REMARK 3 DIHEDRAL : 12.397 1027 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): 12.7172 -18.7607 -14.4207 REMARK 3 T TENSOR REMARK 3 T11: 0.2063 T22: 0.2081 REMARK 3 T33: 0.1951 T12: 0.0415 REMARK 3 T13: 0.0038 T23: -0.0284 REMARK 3 L TENSOR REMARK 3 L11: 1.0219 L22: 0.9225 REMARK 3 L33: 1.0404 L12: -0.4769 REMARK 3 L13: 0.4825 L23: -0.3704 REMARK 3 S TENSOR REMARK 3 S11: 0.0512 S12: 0.1623 S13: -0.1505 REMARK 3 S21: -0.0457 S22: -0.1045 S23: -0.0777 REMARK 3 S31: 0.1815 S32: 0.2048 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 232:289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.0623 8.2308 -16.9469 REMARK 3 T TENSOR REMARK 3 T11: 0.2214 T22: 0.2482 REMARK 3 T33: 0.3402 T12: 0.0057 REMARK 3 T13: 0.0783 T23: 0.0764 REMARK 3 L TENSOR REMARK 3 L11: 0.3791 L22: 0.5545 REMARK 3 L33: 0.3732 L12: 0.0963 REMARK 3 L13: -0.0034 L23: 0.1706 REMARK 3 S TENSOR REMARK 3 S11: 0.0904 S12: 0.1091 S13: 0.3026 REMARK 3 S21: -0.0881 S22: -0.0272 S23: -0.3235 REMARK 3 S31: -0.1675 S32: 0.0598 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 290:423 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.1912 8.5686 -0.5382 REMARK 3 T TENSOR REMARK 3 T11: 0.1777 T22: 0.1628 REMARK 3 T33: 0.2032 T12: -0.0047 REMARK 3 T13: 0.0199 T23: -0.0269 REMARK 3 L TENSOR REMARK 3 L11: 1.6102 L22: 1.0050 REMARK 3 L33: 0.3415 L12: -0.1641 REMARK 3 L13: -0.1394 L23: -0.2387 REMARK 3 S TENSOR REMARK 3 S11: 0.1142 S12: -0.1144 S13: 0.3391 REMARK 3 S21: 0.1254 S22: -0.0739 S23: -0.0790 REMARK 3 S31: -0.0487 S32: -0.0357 S33: 0.0123 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 424:494 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.2656 -10.5425 -11.3272 REMARK 3 T TENSOR REMARK 3 T11: 0.1520 T22: 0.1789 REMARK 3 T33: 0.1544 T12: -0.0007 REMARK 3 T13: -0.0066 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 0.9243 L22: 0.9655 REMARK 3 L33: 1.0502 L12: -0.0869 REMARK 3 L13: -0.3770 L23: 0.4181 REMARK 3 S TENSOR REMARK 3 S11: 0.0366 S12: 0.1767 S13: -0.0819 REMARK 3 S21: 0.0078 S22: -0.0697 S23: 0.1210 REMARK 3 S31: -0.0068 S32: -0.1549 S33: -0.0002 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): 0.6152 -6.1247 -22.2732 REMARK 3 T TENSOR REMARK 3 T11: 0.2700 T22: 0.3117 REMARK 3 T33: 0.1797 T12: 0.0188 REMARK 3 T13: -0.0051 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.4652 L22: 0.2397 REMARK 3 L33: 0.2578 L12: -0.0948 REMARK 3 L13: 0.1525 L23: -0.1135 REMARK 3 S TENSOR REMARK 3 S11: 0.0677 S12: 0.2851 S13: 0.0352 REMARK 3 S21: -0.2960 S22: -0.0176 S23: -0.0028 REMARK 3 S31: -0.0099 S32: -0.0810 S33: 0.0410 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 6P1R 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_1000241731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-15 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50827 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 40.6000 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39300 REMARK 200 FOR SHELL : 2.960 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 (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH 7.5, 100MM NACL, 10% REMARK 280 W/V 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 29.94450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.24450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.24450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.94450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.38500 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: 5520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 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 HIS A 365 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 173 CG CD OE1 OE2 REMARK 470 LEU A 196 CD1 CD2 REMARK 470 GLN A 200 CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 GLU A 223 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 LEU A 280 CD1 CD2 REMARK 470 GLN A 300 CD OE1 NE2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 CD OE1 NE2 REMARK 470 GLN A 357 OE1 NE2 REMARK 470 GLN A 364 CD OE1 NE2 REMARK 470 TRP A 434 CE3 CZ2 CZ3 CH2 REMARK 470 GLU A 465 CD OE1 OE2 REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLN A 471 OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC T 1 O3' DC T 1 C3' -0.045 REMARK 500 DT P 3 O3' DT P 3 C3' -0.046 REMARK 500 DG D 1 P DG D 1 OP3 -0.118 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 DT T 6 O4' - C1' - N1 ANGL. DEV. = 2.9 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 ASN A 153 40.63 -141.38 REMARK 500 GLN A 268 59.96 -118.56 REMARK 500 LEU A 310 95.03 -160.14 REMARK 500 THR A 318 -150.61 -123.26 REMARK 500 THR A 318 -158.00 -131.53 REMARK 500 SER A 411 -145.44 -169.33 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 87.2 93.8 REMARK 620 4 DT P 3 OP1 172.0 90.6 92.5 REMARK 620 5 DT P 3 OP1 165.8 96.5 89.0 6.7 REMARK 620 6 HOH P 102 O 84.1 172.7 79.1 88.0 81.7 REMARK 620 7 HOH P 113 O 91.8 96.2 170.0 87.2 89.6 90.9 REMARK 620 N 1 2 3 4 5 6 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 100.2 REMARK 620 3 ASP A 418 OD2 89.5 98.3 REMARK 620 4 ZAN A 501 O2A 90.2 90.1 171.4 REMARK 620 5 HOH A 662 O 173.1 84.6 84.8 94.8 REMARK 620 6 DA P 4 O3' 170.3 88.2 84.4 94.7 3.6 REMARK 620 7 HOH P 105 O 89.7 167.5 89.2 82.2 86.2 82.6 REMARK 620 N 1 2 3 4 5 6 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 94.7 REMARK 620 3 ZAN A 501 O2A 94.7 90.3 REMARK 620 4 ZAN A 501 O2B 171.2 93.2 89.3 REMARK 620 5 ZAN A 501 O2G 86.2 178.3 91.1 85.9 REMARK 620 6 HOH A 725 O 86.2 87.4 177.6 90.1 91.2 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 ZAN 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 DBREF 6P1R A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 6P1R T 1 9 PDB 6P1R 6P1R 1 9 DBREF 6P1R P 1 4 PDB 6P1R 6P1R 1 4 DBREF 6P1R D 1 4 PDB 6P1R 6P1R 1 4 SEQADV 6P1R GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1R SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1R ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1R ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1R ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1R A UNP Q9NP87 PRO 398 DELETION SEQADV 6P1R A UNP Q9NP87 GLY 399 DELETION SEQADV 6P1R A UNP Q9NP87 ALA 400 DELETION SEQADV 6P1R A UNP Q9NP87 ALA 401 DELETION SEQADV 6P1R A UNP Q9NP87 VAL 402 DELETION SEQADV 6P1R A UNP Q9NP87 GLY 403 DELETION SEQADV 6P1R A UNP Q9NP87 GLY 404 DELETION SEQADV 6P1R A UNP Q9NP87 SER 405 DELETION SEQADV 6P1R A UNP Q9NP87 THR 406 DELETION SEQADV 6P1R A UNP Q9NP87 ARG 407 DELETION SEQADV 6P1R A UNP Q9NP87 PRO 408 DELETION SEQADV 6P1R A UNP Q9NP87 CYS 409 DELETION SEQADV 6P1R 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 ZAN A 501 31 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 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM ZAN 5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 ZAN PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN EPE HEPES FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 5 ZAN C10 H17 N6 O12 P3 FORMUL 6 MG 2(MG 2+) FORMUL 8 NA NA 1+ FORMUL 9 CL 3(CL 1-) FORMUL 12 EPE C8 H18 N2 O4 S FORMUL 13 HOH *319(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 ALA A 188 1 17 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 2.34 LINK O VAL A 246 NA NA A 504 1555 1555 2.29 LINK OD2 ASP A 330 MG MG A 502 1555 1555 1.99 LINK OD1 ASP A 330 MG MG A 503 1555 1555 2.02 LINK OD1 ASP A 332 MG MG A 502 1555 1555 2.02 LINK OD2 ASP A 332 MG MG A 503 1555 1555 2.01 LINK OD2 ASP A 418 MG MG A 502 1555 1555 2.00 LINK O2A ZAN A 501 MG MG A 502 1555 1555 2.32 LINK O2A ZAN A 501 MG MG A 503 1555 1555 2.17 LINK O2B ZAN A 501 MG MG A 503 1555 1555 2.09 LINK O2G ZAN A 501 MG MG A 503 1555 1555 2.16 LINK MG MG A 502 O BHOH A 662 1555 1555 2.00 LINK MG MG A 502 O3'A DA P 4 1555 1555 2.34 LINK MG MG A 502 O HOH P 105 1555 1555 2.11 LINK MG MG A 503 O HOH A 725 1555 1555 2.10 LINK NA NA A 504 OP1A DT P 3 1555 1555 2.64 LINK NA NA A 504 OP1B DT P 3 1555 1555 2.37 LINK NA NA A 504 O HOH P 102 1555 1555 2.59 LINK NA NA A 504 O HOH P 113 1555 1555 2.38 CISPEP 1 GLY A 436 SER A 437 0 -6.64 SITE 1 AC1 27 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC1 27 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC1 27 GLY A 433 TRP A 434 THR A 435 GLY A 436 SITE 4 AC1 27 LYS A 438 MG A 502 MG A 503 HOH A 621 SITE 5 AC1 27 HOH A 655 HOH A 662 HOH A 693 HOH A 704 SITE 6 AC1 27 HOH A 725 HOH A 729 HOH A 737 HOH A 758 SITE 7 AC1 27 DA P 4 HOH P 105 8OG T 5 SITE 1 AC2 8 ASP A 330 ASP A 332 ASP A 418 ZAN A 501 SITE 2 AC2 8 MG A 503 HOH A 662 DA P 4 HOH P 105 SITE 1 AC3 5 ASP A 330 ASP A 332 ZAN A 501 MG A 502 SITE 2 AC3 5 HOH A 725 SITE 1 AC4 6 THR A 241 ILE A 243 VAL A 246 DT P 3 SITE 2 AC4 6 HOH P 102 HOH P 113 SITE 1 AC5 3 ASN A 457 SER A 458 DA T 7 SITE 1 AC6 2 SER A 425 GLN A 426 SITE 1 AC7 4 SER A 474 GLU A 475 HOH A 797 HOH A 866 SITE 1 AC8 5 LYS A 325 LEU A 326 GLN A 327 HOH A 623 SITE 2 AC8 5 HOH A 780 CRYST1 59.889 68.770 110.489 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 0.016698 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014541 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009051 0.00000