HEADER TRANSFERASE/DNA 20-FEB-15 4YD1 TITLE TERNARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH 2-NT GAPPED DNA TITLE 2 SUBSTRATE AND AN INCOMING NONHYDROLYZABLE DUMPNPP 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 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*G)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*GP*TP*A)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 18 CHAIN: D; COMPND 19 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 4YD1 1 LINK REVDAT 5 18-DEC-19 4YD1 1 REMARK REVDAT 4 20-SEP-17 4YD1 1 JRNL REMARK REVDAT 3 26-AUG-15 4YD1 1 JRNL REVDAT 2 19-AUG-15 4YD1 1 JRNL REVDAT 1 05-AUG-15 4YD1 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. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 49927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2497 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 24.9742 - 4.5745 1.00 2829 148 0.1650 0.1877 REMARK 3 2 4.5745 - 3.6345 1.00 2697 143 0.1298 0.1364 REMARK 3 3 3.6345 - 3.1761 1.00 2670 139 0.1435 0.1641 REMARK 3 4 3.1761 - 2.8862 1.00 2651 141 0.1718 0.2034 REMARK 3 5 2.8862 - 2.6796 0.99 2659 140 0.1829 0.2141 REMARK 3 6 2.6796 - 2.5218 0.99 2616 139 0.1771 0.2417 REMARK 3 7 2.5218 - 2.3956 1.00 2619 138 0.1676 0.2054 REMARK 3 8 2.3956 - 2.2914 1.00 2636 139 0.1531 0.1520 REMARK 3 9 2.2914 - 2.2032 1.00 2633 137 0.1497 0.2016 REMARK 3 10 2.2032 - 2.1272 1.00 2609 138 0.1555 0.2058 REMARK 3 11 2.1272 - 2.0608 1.00 2637 134 0.1650 0.1815 REMARK 3 12 2.0608 - 2.0019 1.00 2593 143 0.1670 0.2048 REMARK 3 13 2.0019 - 1.9492 1.00 2600 137 0.1690 0.1983 REMARK 3 14 1.9492 - 1.9017 1.00 2626 137 0.1759 0.2173 REMARK 3 15 1.9017 - 1.8584 1.00 2606 137 0.1999 0.2333 REMARK 3 16 1.8584 - 1.8189 1.00 2598 137 0.2209 0.2729 REMARK 3 17 1.8189 - 1.7825 1.00 2608 137 0.2204 0.2655 REMARK 3 18 1.7825 - 1.7489 0.98 2543 133 0.2336 0.2692 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) : 0.190 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 3218 REMARK 3 ANGLE : 1.238 4449 REMARK 3 CHIRALITY : 0.059 486 REMARK 3 PLANARITY : 0.007 519 REMARK 3 DIHEDRAL : 14.016 1034 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): 12.3796 -18.7138 -14.1580 REMARK 3 T TENSOR REMARK 3 T11: 0.1420 T22: 0.1627 REMARK 3 T33: 0.1405 T12: 0.0596 REMARK 3 T13: -0.0013 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 1.4922 L22: 1.4161 REMARK 3 L33: 1.4392 L12: -0.1749 REMARK 3 L13: -0.0248 L23: -0.3894 REMARK 3 S TENSOR REMARK 3 S11: 0.0509 S12: 0.1966 S13: -0.1788 REMARK 3 S21: -0.1315 S22: -0.1089 S23: -0.1354 REMARK 3 S31: 0.1865 S32: 0.3013 S33: 0.0594 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): 15.6396 8.1073 -17.2829 REMARK 3 T TENSOR REMARK 3 T11: 0.1870 T22: 0.2151 REMARK 3 T33: 0.2160 T12: -0.0247 REMARK 3 T13: 0.0507 T23: 0.0543 REMARK 3 L TENSOR REMARK 3 L11: 1.8487 L22: 1.5867 REMARK 3 L33: 2.5711 L12: -0.3844 REMARK 3 L13: -1.2627 L23: 0.9736 REMARK 3 S TENSOR REMARK 3 S11: 0.0869 S12: 0.1669 S13: 0.2279 REMARK 3 S21: -0.3253 S22: -0.0060 S23: -0.3902 REMARK 3 S31: -0.2834 S32: 0.2652 S33: -0.0397 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): -3.9208 8.3540 -1.8139 REMARK 3 T TENSOR REMARK 3 T11: 0.1278 T22: 0.0907 REMARK 3 T33: 0.0926 T12: 0.0029 REMARK 3 T13: 0.0117 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 3.0838 L22: 2.4783 REMARK 3 L33: 0.6509 L12: 0.0399 REMARK 3 L13: -0.0733 L23: -0.2335 REMARK 3 S TENSOR REMARK 3 S11: 0.0534 S12: -0.0409 S13: 0.2454 REMARK 3 S21: 0.0777 S22: -0.0316 S23: 0.1203 REMARK 3 S31: -0.1132 S32: -0.0550 S33: -0.0041 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): -11.5573 -11.0299 -11.1775 REMARK 3 T TENSOR REMARK 3 T11: 0.0862 T22: 0.0784 REMARK 3 T33: 0.1013 T12: -0.0070 REMARK 3 T13: -0.0060 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 2.3395 L22: 1.8132 REMARK 3 L33: 2.1063 L12: -0.1164 REMARK 3 L13: 0.1705 L23: 0.3555 REMARK 3 S TENSOR REMARK 3 S11: 0.0469 S12: 0.1911 S13: -0.0932 REMARK 3 S21: -0.1047 S22: -0.0608 S23: 0.2073 REMARK 3 S31: 0.0773 S32: -0.1671 S33: 0.0049 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: NULL REMARK 3 ORIGIN FOR THE GROUP (A): -1.2484 -6.5604 -23.8428 REMARK 3 T TENSOR REMARK 3 T11: 0.1754 T22: 0.2277 REMARK 3 T33: 0.1017 T12: 0.0094 REMARK 3 T13: -0.0100 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 1.9310 L22: 1.0134 REMARK 3 L33: 2.3305 L12: -0.3591 REMARK 3 L13: -0.3242 L23: 0.3202 REMARK 3 S TENSOR REMARK 3 S11: 0.0995 S12: 0.3217 S13: 0.0071 REMARK 3 S21: -0.2960 S22: -0.0912 S23: 0.0154 REMARK 3 S31: -0.0707 S32: -0.0518 S33: -0.0053 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 4YD1 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_1000207243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-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 : 49927 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : 26.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.580 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: 4YCX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 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 30.12950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.49400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.52100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.49400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.12950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.52100 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: 6440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 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 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 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 ARG A 227 CD NE CZ NH1 NH2 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 300 CD OE1 NE2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 LYS A 339 CG CD CE NZ REMARK 470 GLU A 465 CG CD OE1 OE2 REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLN A 471 CD OE1 NE2 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 NE2 GLN A 342 O HOH A 701 2.14 REMARK 500 O HOH A 719 O HOH A 963 2.15 REMARK 500 O HOH A 1064 O HOH A 1072 2.16 REMARK 500 O HOH T 217 O HOH T 236 2.16 REMARK 500 NZ LYS A 325 O HOH A 702 2.17 REMARK 500 OE1 GLN A 275 O HOH A 703 2.18 REMARK 500 O HOH T 204 O HOH T 245 2.18 REMARK 500 O HOH A 763 O HOH A 870 2.18 REMARK 500 O HOH A 790 O HOH T 219 2.19 REMARK 500 O HOH A 1020 O HOH A 1039 2.19 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 DG D 1 P DG D 1 OP3 -0.125 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG T 10 O4' - C1' - N9 ANGL. DEV. = 2.5 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 HIS A 151 -157.28 -154.63 REMARK 500 ASN A 153 42.77 -141.71 REMARK 500 THR A 318 -152.45 -128.28 REMARK 500 SER A 411 -151.61 -161.55 REMARK 500 ASN A 493 48.93 -88.30 REMARK 500 REMARK 500 REMARK: NULL 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 612 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 99.4 REMARK 620 3 VAL A 246 O 88.5 93.1 REMARK 620 4 HOH A 838 O 78.1 163.7 70.8 REMARK 620 5 HOH A 982 O 86.0 97.3 168.9 98.6 REMARK 620 6 HOH P 114 O 98.2 141.6 121.2 54.2 50.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 101.9 REMARK 620 3 ASP A 418 OD2 88.7 97.5 REMARK 620 4 DUP A 607 O1A 93.0 89.2 172.6 REMARK 620 5 HOH A 770 O 86.3 168.5 90.6 82.3 REMARK 620 6 DA P 4 O3' 171.7 84.4 85.1 92.4 88.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 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 DUP A 607 O3G 85.2 178.3 REMARK 620 4 DUP A 607 O1A 100.0 89.8 91.1 REMARK 620 5 DUP A 607 O2B 167.9 90.8 90.6 91.4 REMARK 620 6 HOH A 850 O 82.4 88.3 90.8 177.1 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG T 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH T 207 O REMARK 620 2 HOH T 216 O 91.5 REMARK 620 3 HOH T 223 O 97.0 100.4 REMARK 620 4 HOH T 247 O 171.4 95.7 86.4 REMARK 620 5 HOH T 255 O 80.8 165.1 93.1 91.1 REMARK 620 6 HOH D 116 O 86.7 85.6 172.8 89.0 81.3 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 MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DUP A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG T 101 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 THE SAME DNA REMARK 900 SUBSTRATE REMARK 900 RELATED ID: 4YD1 RELATED DB: PDB DBREF 4YD1 A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 4YD1 T 1 10 PDB 4YD1 4YD1 1 10 DBREF 4YD1 P 1 4 PDB 4YD1 4YD1 1 4 DBREF 4YD1 D 1 4 PDB 4YD1 4YD1 1 4 SEQADV 4YD1 GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD1 SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD1 ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD1 ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD1 ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 4YD1 A UNP Q9NP87 PRO 398 DELETION SEQADV 4YD1 A UNP Q9NP87 GLY 399 DELETION SEQADV 4YD1 A UNP Q9NP87 ALA 400 DELETION SEQADV 4YD1 A UNP Q9NP87 ALA 401 DELETION SEQADV 4YD1 A UNP Q9NP87 VAL 402 DELETION SEQADV 4YD1 A UNP Q9NP87 GLY 403 DELETION SEQADV 4YD1 A UNP Q9NP87 GLY 404 DELETION SEQADV 4YD1 A UNP Q9NP87 SER 405 DELETION SEQADV 4YD1 A UNP Q9NP87 THR 406 DELETION SEQADV 4YD1 A UNP Q9NP87 ARG 407 DELETION SEQADV 4YD1 A UNP Q9NP87 PRO 408 DELETION SEQADV 4YD1 A UNP Q9NP87 CYS 409 DELETION SEQADV 4YD1 GLY A 410 UNP Q9NP87 PRO 410 ENGINEERED MUTATION 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 4 DC DG DT DA SEQRES 1 D 4 DG DC DC DG HET MG A 601 1 HET MG A 602 1 HET EDO A 603 4 HET GOL A 604 6 HET GOL A 605 6 HET EDO A 606 4 HET DUP A 607 28 HET CL A 608 1 HET CL A 609 1 HET CL A 610 1 HET CL A 611 1 HET NA A 612 1 HET MG T 101 1 HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MG 3(MG 2+) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 8 GOL 2(C3 H8 O3) FORMUL 11 DUP C9 H16 N3 O13 P3 FORMUL 12 CL 4(CL 1-) FORMUL 16 NA NA 1+ FORMUL 18 HOH *468(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 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 ASP A 356 1 11 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 ASP A 330 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 GLU A 386 GLN A 396 -1 N PHE A 392 O VAL A 415 SHEET 5 AA2 5 ILE A 360 GLN A 366 -1 N GLN A 366 O ARG A 387 SHEET 1 AA3 3 TRP A 455 ASN A 457 0 SHEET 2 AA3 3 GLY A 460 ASP A 463 -1 O PHE A 462 N TRP A 455 SHEET 3 AA3 3 THR A 468 PHE A 469 -1 O THR A 468 N ASP A 463 LINK O THR A 241 NA NA A 612 1555 1555 2.56 LINK O ILE A 243 NA NA A 612 1555 1555 2.44 LINK O VAL A 246 NA NA A 612 1555 1555 2.43 LINK OD2 ASP A 330 MG MG A 601 1555 1555 2.06 LINK OD1 ASP A 330 MG MG A 602 1555 1555 2.04 LINK OD1 ASP A 332 MG MG A 601 1555 1555 2.02 LINK OD2 ASP A 332 MG MG A 602 1555 1555 2.04 LINK OD2 ASP A 418 MG MG A 601 1555 1555 2.01 LINK MG MG A 601 O1A DUP A 607 1555 1555 2.31 LINK MG MG A 601 O HOH A 770 1555 1555 2.11 LINK MG MG A 601 O3' DA P 4 1555 1555 2.22 LINK MG MG A 602 O3G DUP A 607 1555 1555 2.03 LINK MG MG A 602 O1A DUP A 607 1555 1555 2.13 LINK MG MG A 602 O2B DUP A 607 1555 1555 2.03 LINK MG MG A 602 O HOH A 850 1555 1555 2.17 LINK NA NA A 612 O HOH A 838 1555 1555 2.33 LINK NA NA A 612 O HOH A 982 1555 1555 2.38 LINK NA NA A 612 O HOH P 114 1555 1555 2.84 LINK MG MG T 101 O HOH T 207 1555 1555 2.10 LINK MG MG T 101 O HOH T 216 1555 1555 1.92 LINK MG MG T 101 O HOH T 223 1555 1555 1.98 LINK MG MG T 101 O HOH T 247 1555 3544 2.28 LINK MG MG T 101 O HOH T 255 1555 1555 2.14 LINK MG MG T 101 O HOH D 116 1555 1555 2.14 CISPEP 1 GLY A 436 SER A 437 0 -5.12 SITE 1 AC1 7 ASP A 330 ASP A 332 ASP A 418 MG A 602 SITE 2 AC1 7 DUP A 607 HOH A 770 DA P 4 SITE 1 AC2 5 ASP A 330 ASP A 332 MG A 601 DUP A 607 SITE 2 AC2 5 HOH A 850 SITE 1 AC3 4 PRO A 190 SER A 191 PRO A 192 GLN A 198 SITE 1 AC4 5 TRP A 455 PHE A 462 HOH A 706 HOH A 708 SITE 2 AC4 5 HOH T 202 SITE 1 AC5 2 HOH A 704 HOH A 717 SITE 1 AC6 6 GLY A 433 ARG A 445 SER A 458 DUP A 607 SITE 2 AC6 6 HOH A 786 DA P 4 SITE 1 AC7 27 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC7 27 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC7 27 GLY A 433 TRP A 434 GLY A 436 MG A 601 SITE 4 AC7 27 MG A 602 EDO A 606 HOH A 702 HOH A 749 SITE 5 AC7 27 HOH A 770 HOH A 773 HOH A 797 HOH A 814 SITE 6 AC7 27 HOH A 834 HOH A 850 HOH A 904 HOH A 922 SITE 7 AC7 27 HOH A 932 DA P 4 DA T 5 SITE 1 AC8 3 SER A 172 GLY A 174 ARG A 175 SITE 1 AC9 4 SER A 474 GLU A 475 HOH A 926 HOH A 963 SITE 1 AD1 1 LEU A 326 SITE 1 AD2 4 PHE A 385 ARG A 387 TRP A 434 HOH A 759 SITE 1 AD3 7 THR A 241 ILE A 243 VAL A 246 HOH A 838 SITE 2 AD3 7 HOH A 982 DT P 3 HOH P 114 SITE 1 AD4 6 HOH D 116 HOH T 207 HOH T 216 HOH T 223 SITE 2 AD4 6 HOH T 247 HOH T 255 CRYST1 60.259 69.042 116.988 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 0.016595 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014484 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008548 0.00000