HEADER TRANSFERASE/DNA 20-FEB-15 4YD2 TITLE NICKED COMPLEX OF HUMAN DNA POLYMERASE MU WITH 2-NT GAPPED DNA TITLE 2 SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 134-494; 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*AP*T)-3'); COMPND 11 CHAIN: T; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*T)-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 19 CHAIN: D; COMPND 20 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_TAXID: 9606 KEYWDS POLYMERASE, DNA REPAIR, NHEJ, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.F.MOON,R.A.GOSAVI,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK REVDAT 6 27-SEP-23 4YD2 1 LINK REVDAT 5 18-DEC-19 4YD2 1 REMARK REVDAT 4 20-SEP-17 4YD2 1 JRNL REMARK REVDAT 3 26-AUG-15 4YD2 1 JRNL REVDAT 2 19-AUG-15 4YD2 1 JRNL REVDAT 1 05-AUG-15 4YD2 0 JRNL AUTH A.F.MOON,R.A.GOSAVI,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK JRNL TITL CREATIVE TEMPLATE-DEPENDENT SYNTHESIS BY HUMAN POLYMERASE JRNL TITL 2 MU. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 E4530 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 26240373 JRNL DOI 10.1073/PNAS.1505798112 REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 17102 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 858 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 22.6143 - 4.4806 0.99 2917 154 0.1841 0.2321 REMARK 3 2 4.4806 - 3.5608 1.00 2797 146 0.1745 0.1718 REMARK 3 3 3.5608 - 3.1120 1.00 2768 151 0.2043 0.2529 REMARK 3 4 3.1120 - 2.8281 0.99 2740 135 0.2673 0.2856 REMARK 3 5 2.8281 - 2.6257 0.99 2721 144 0.2905 0.2803 REMARK 3 6 2.6257 - 2.4711 0.84 2301 128 0.2804 0.4270 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.260 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 : 0.002 2983 REMARK 3 ANGLE : 0.505 4123 REMARK 3 CHIRALITY : 0.020 455 REMARK 3 PLANARITY : 0.002 491 REMARK 3 DIHEDRAL : 11.898 971 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): 12.1668 -18.7676 -14.1766 REMARK 3 T TENSOR REMARK 3 T11: 0.2213 T22: 0.2754 REMARK 3 T33: 0.2125 T12: 0.0460 REMARK 3 T13: -0.0377 T23: -0.0313 REMARK 3 L TENSOR REMARK 3 L11: 3.7456 L22: 1.7768 REMARK 3 L33: 3.3530 L12: -0.6306 REMARK 3 L13: -1.4212 L23: -0.8959 REMARK 3 S TENSOR REMARK 3 S11: 0.1495 S12: 0.4437 S13: -0.2476 REMARK 3 S21: -0.2007 S22: -0.1651 S23: -0.0055 REMARK 3 S31: 0.1880 S32: 0.2967 S33: 0.0168 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 232:289 REMARK 3 ORIGIN FOR THE GROUP (A): 16.3378 8.0830 -16.8811 REMARK 3 T TENSOR REMARK 3 T11: 0.3450 T22: 0.3670 REMARK 3 T33: 0.4018 T12: 0.0114 REMARK 3 T13: 0.0772 T23: 0.1311 REMARK 3 L TENSOR REMARK 3 L11: 2.3641 L22: 2.6622 REMARK 3 L33: 4.6598 L12: 0.4625 REMARK 3 L13: -1.2625 L23: 0.7429 REMARK 3 S TENSOR REMARK 3 S11: 0.1309 S12: 0.3607 S13: 0.5457 REMARK 3 S21: -0.5108 S22: -0.0593 S23: -0.2874 REMARK 3 S31: -0.3551 S32: 0.3118 S33: -0.0628 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 290:423 REMARK 3 ORIGIN FOR THE GROUP (A): -2.8261 8.6543 -0.3445 REMARK 3 T TENSOR REMARK 3 T11: 0.2062 T22: 0.1942 REMARK 3 T33: 0.2247 T12: 0.0199 REMARK 3 T13: -0.0046 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 4.9216 L22: 4.2024 REMARK 3 L33: 0.0303 L12: 0.1882 REMARK 3 L13: -0.5253 L23: 0.0953 REMARK 3 S TENSOR REMARK 3 S11: 0.1543 S12: -0.1789 S13: 0.6045 REMARK 3 S21: -0.0119 S22: -0.1109 S23: -0.0601 REMARK 3 S31: -0.0866 S32: -0.0464 S33: -0.0349 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 424:494 REMARK 3 ORIGIN FOR THE GROUP (A): -11.5277 -10.6842 -11.2611 REMARK 3 T TENSOR REMARK 3 T11: 0.1777 T22: 0.2200 REMARK 3 T33: 0.2146 T12: -0.0244 REMARK 3 T13: -0.0258 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 2.8247 L22: 2.2311 REMARK 3 L33: 3.0371 L12: -1.3149 REMARK 3 L13: -0.0024 L23: 0.3846 REMARK 3 S TENSOR REMARK 3 S11: 0.0941 S12: 0.5298 S13: -0.0717 REMARK 3 S21: -0.1526 S22: -0.1503 S23: 0.3065 REMARK 3 S31: -0.0202 S32: -0.1358 S33: 0.0386 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 0.5586 -9.1799 -23.5878 REMARK 3 T TENSOR REMARK 3 T11: 0.4251 T22: 0.5939 REMARK 3 T33: 0.2871 T12: 0.0348 REMARK 3 T13: -0.0870 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 2.7538 L22: 1.6119 REMARK 3 L33: 3.7937 L12: 0.8048 REMARK 3 L13: -0.4588 L23: -2.1336 REMARK 3 S TENSOR REMARK 3 S11: 0.2270 S12: 0.9243 S13: 0.0934 REMARK 3 S21: -0.6054 S22: -0.2438 S23: 0.2614 REMARK 3 S31: -0.0813 S32: -0.3678 S33: 0.0022 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 4YD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207247. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17102 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 16.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.820 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: 4YD1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 20% PEG8K, 0.2M MGCL2, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 30.04150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.48850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.48850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.04150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.35000 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: 4480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 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 364 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 465 ALA A 384 REMARK 465 PHE A 385 REMARK 465 DA T 8 REMARK 465 DC T 9 REMARK 465 DG T 10 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 LEU A 196 CG CD1 CD2 REMARK 470 GLN A 200 CG CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 ARG A 211 NE CZ NH1 NH2 REMARK 470 GLN A 214 CD OE1 NE2 REMARK 470 GLU A 223 CG CD OE1 OE2 REMARK 470 ARG A 227 CD NE CZ NH1 NH2 REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 LEU A 259 CD1 CD2 REMARK 470 GLU A 267 CG 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 LYS A 277 CE NZ 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 HIS A 329 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 339 CG CD CE NZ REMARK 470 GLN A 357 OE1 NE2 REMARK 470 LYS A 450 CG CD CE NZ REMARK 470 GLU A 465 CG 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 D 1 P DG D 1 OP3 -0.127 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 HIS A 151 -153.78 -142.82 REMARK 500 ARG A 260 -32.74 -131.63 REMARK 500 LYS A 271 32.38 -98.51 REMARK 500 THR A 318 -149.10 -120.93 REMARK 500 PRO A 397 99.10 -55.74 REMARK 500 SER A 411 -148.07 -158.65 REMARK 500 ASN A 493 47.07 -86.08 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 PPV A 507 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 505 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 97.6 REMARK 620 3 VAL A 246 O 67.6 74.0 REMARK 620 4 HOH A 659 O 76.2 128.2 55.8 REMARK 620 5 DT P 3 OP1 129.3 81.2 63.4 66.3 REMARK 620 6 HOH P 102 O 134.6 126.6 129.1 82.9 74.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD1 78.6 REMARK 620 3 ASP A 418 OD2 130.3 83.4 REMARK 620 4 DA P 4 O3' 135.7 89.3 89.4 REMARK 620 5 DT P 5 OP1 75.0 80.6 146.2 60.9 REMARK 620 N 1 2 3 4 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 ASP A 330 OD1 REMARK 620 2 ASP A 330 OD2 49.3 REMARK 620 3 ASP A 332 OD2 68.1 116.4 REMARK 620 4 PPV A 507 O22 133.0 95.0 125.2 REMARK 620 5 PPV A 507 O32 143.3 149.1 79.6 55.8 REMARK 620 6 HOH A 632 O 83.2 111.8 64.5 143.7 98.9 REMARK 620 7 DT P 5 OP1 75.0 80.1 73.8 68.6 79.6 137.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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 NA 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 PPV A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YCX RELATED DB: PDB REMARK 900 4YCX CONTAINS THE SAME PROTEIN IN BINARY COMPLEX WITH A 2-NT GAPPED REMARK 900 DNA SUBSTRATE REMARK 900 RELATED ID: 4YD1 RELATED DB: PDB DBREF 4YD2 A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 4YD2 T 1 10 PDB 4YD2 4YD2 1 10 DBREF 4YD2 P 1 5 PDB 4YD2 4YD2 1 5 DBREF 4YD2 D 1 4 PDB 4YD2 4YD2 1 4 SEQADV 4YD2 GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD2 SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD2 ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD2 ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD2 ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD2 A UNP Q9NP87 PRO 398 DELETION SEQADV 4YD2 A UNP Q9NP87 GLY 399 DELETION SEQADV 4YD2 A UNP Q9NP87 ALA 400 DELETION SEQADV 4YD2 A UNP Q9NP87 ALA 401 DELETION SEQADV 4YD2 A UNP Q9NP87 VAL 402 DELETION SEQADV 4YD2 A UNP Q9NP87 GLY 403 DELETION SEQADV 4YD2 A UNP Q9NP87 GLY 404 DELETION SEQADV 4YD2 A UNP Q9NP87 SER 405 DELETION SEQADV 4YD2 A UNP Q9NP87 THR 406 DELETION SEQADV 4YD2 A UNP Q9NP87 ARG 407 DELETION SEQADV 4YD2 A UNP Q9NP87 PRO 408 DELETION SEQADV 4YD2 A UNP Q9NP87 CYS 409 DELETION SEQADV 4YD2 GLY A 410 UNP Q9NP87 INSERTION 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 10 DC DG DG DC DA DA DT DA DC DG SEQRES 1 P 5 DC DG DT DA DT SEQRES 1 D 4 DG DC DC DG HET NA A 501 1 HET CL A 502 1 HET CL A 503 1 HET NA A 504 1 HET NA A 505 1 HET CL A 506 1 HET PPV A 507 5 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PPV PYROPHOSPHATE FORMUL 5 NA 3(NA 1+) FORMUL 6 CL 3(CL 1-) FORMUL 11 PPV H4 O7 P2 FORMUL 12 HOH *142(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 LEU A 346 GLN A 357 1 12 HELIX 16 AB7 GLN A 426 GLY A 436 1 11 HELIX 17 AB8 SER A 437 GLY A 453 1 17 HELIX 18 AB9 SER A 474 LEU A 482 1 9 HELIX 19 AC1 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 TYR A 362 O ILE A 391 SHEET 1 AA3 3 TRP A 455 LEU A 456 0 SHEET 2 AA3 3 LEU A 461 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 505 1555 1555 2.47 LINK O ILE A 243 NA NA A 505 1555 1555 2.51 LINK O VAL A 246 NA NA A 505 1555 1555 3.17 LINK OD1 ASP A 330 NA NA A 501 1555 1555 2.51 LINK OD1 ASP A 330 NA NA A 504 1555 1555 2.50 LINK OD2 ASP A 330 NA NA A 504 1555 1555 2.74 LINK OD1 ASP A 332 NA NA A 501 1555 1555 2.50 LINK OD2 ASP A 332 NA NA A 504 1555 1555 2.65 LINK OD2 ASP A 418 NA NA A 501 1555 1555 2.35 LINK NA NA A 501 O3' DA P 4 1555 1555 2.52 LINK NA NA A 501 OP1 DT P 5 1555 1555 2.40 LINK NA NA A 504 O22 PPV A 507 1555 1555 2.81 LINK NA NA A 504 O32 PPV A 507 1555 1555 2.51 LINK NA NA A 504 O HOH A 632 1555 1555 2.42 LINK NA NA A 504 OP1 DT P 5 1555 1555 2.41 LINK NA NA A 505 O HOH A 659 1555 1555 3.02 LINK NA NA A 505 OP1 DT P 3 1555 1555 2.93 LINK NA NA A 505 O HOH P 102 1555 1555 2.49 CISPEP 1 GLY A 436 SER A 437 0 0.18 SITE 1 AC1 5 ASP A 330 ASP A 332 ASP A 418 DA P 4 SITE 2 AC1 5 DT P 5 SITE 1 AC2 1 LEU A 326 SITE 1 AC3 5 LEU A 431 SER A 474 GLU A 475 HOH A 610 SITE 2 AC3 5 HOH A 630 SITE 1 AC4 5 ASP A 330 ASP A 332 PPV A 507 HOH A 632 SITE 2 AC4 5 DT P 5 SITE 1 AC5 7 THR A 241 GLN A 242 ILE A 243 VAL A 246 SITE 2 AC5 7 HOH A 659 DT P 3 HOH P 102 SITE 1 AC6 3 SER A 172 GLY A 174 ARG A 175 SITE 1 AC7 9 GLY A 319 GLY A 320 ARG A 323 ASP A 332 SITE 2 AC7 9 NA A 504 HOH A 732 HOH A 733 HOH A 735 SITE 3 AC7 9 DT P 5 CRYST1 60.083 68.700 114.977 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 0.016644 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008697 0.00000