HEADER TRANSFERASE 11-MAR-25 9NPU TITLE PRE-CATALYTIC TERNARY COMPLEX OF DNA POLYMERASE LAMBDA WITH BOUND 1-NT TITLE 2 GAPPED SSB SUBSTRATE CONTAINING TEMPLATE RIBONUCLEOTIDE OPPOSITE TITLE 3 PRIMER TERMINUS, AND INCOMING DUMPNPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 5 KAPPA; COMPND 6 EC: 2.7.7.7,4.2.99.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA/RNA (5'-D(*CP*GP*GP*CP*A)-R(P*G)-D(P*TP*AP*CP*TP*G)- COMPND 10 3'); COMPND 11 CHAIN: T; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*C)-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: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS FAMILY X POLYMERASE, NONHOMOLOGOUS END JOINING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.KAMINSKI,A.J.LUTHMAN,L.C.PEDERSEN,D.A.RAMSDEN,T.A.KUNKEL REVDAT 1 21-JAN-26 9NPU 0 JRNL AUTH A.J.LUTHMAN,K.K.CHIRUVELLA,A.M.KAMINSKI,T.A.KUNKEL, JRNL AUTH 2 L.C.PEDERSEN,D.A.RAMSDEN JRNL TITL NONHOMOLOGOUS END-JOINING USES DISTINCT MECHANISMS TO REPAIR JRNL TITL 2 EACH STRAND OF A DOUBLE STRAND BREAK. JRNL REF NAT COMMUN V. 16 11599 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 41285786 JRNL DOI 10.1038/S41467-025-66528-8 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 60225 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 3029 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 40.9900 - 4.5600 1.00 2807 147 0.1826 0.1919 REMARK 3 2 4.5600 - 3.6200 1.00 2693 139 0.1411 0.1461 REMARK 3 3 3.6200 - 3.1600 1.00 2621 141 0.1539 0.1804 REMARK 3 4 3.1600 - 2.8700 1.00 2642 144 0.1634 0.1851 REMARK 3 5 2.8700 - 2.6700 1.00 2618 126 0.1798 0.2299 REMARK 3 6 2.6700 - 2.5100 1.00 2610 146 0.1656 0.1842 REMARK 3 7 2.5100 - 2.3800 1.00 2608 134 0.1636 0.1707 REMARK 3 8 2.3800 - 2.2800 1.00 2592 134 0.1659 0.2106 REMARK 3 9 2.2800 - 2.1900 1.00 2591 136 0.1723 0.2117 REMARK 3 10 2.1900 - 2.1200 1.00 2588 136 0.1758 0.2086 REMARK 3 11 2.1200 - 2.0500 1.00 2573 146 0.1763 0.2090 REMARK 3 12 2.0500 - 1.9900 1.00 2588 129 0.1802 0.1959 REMARK 3 13 1.9900 - 1.9400 1.00 2567 126 0.1836 0.2056 REMARK 3 14 1.9400 - 1.8900 1.00 2570 151 0.2028 0.2219 REMARK 3 15 1.8900 - 1.8500 1.00 2578 137 0.2029 0.2357 REMARK 3 16 1.8500 - 1.8100 1.00 2560 135 0.2201 0.2369 REMARK 3 17 1.8100 - 1.7700 1.00 2572 134 0.2339 0.2744 REMARK 3 18 1.7700 - 1.7400 1.00 2591 114 0.2372 0.2649 REMARK 3 19 1.7400 - 1.7100 1.00 2511 160 0.2535 0.2550 REMARK 3 20 1.7100 - 1.6800 1.00 2602 130 0.2726 0.2960 REMARK 3 21 1.6800 - 1.6500 1.00 2543 139 0.2968 0.3080 REMARK 3 22 1.6500 - 1.6300 1.00 2571 145 0.3234 0.3755 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.192 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.857 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.75 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 : 0.012 3112 REMARK 3 ANGLE : 1.083 4322 REMARK 3 CHIRALITY : 0.061 479 REMARK 3 PLANARITY : 0.011 480 REMARK 3 DIHEDRAL : 12.969 932 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 239:329 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.571 25.922 -25.877 REMARK 3 T TENSOR REMARK 3 T11: 0.5089 T22: 0.5732 REMARK 3 T33: 0.4274 T12: -0.1308 REMARK 3 T13: 0.1458 T23: -0.0614 REMARK 3 L TENSOR REMARK 3 L11: 0.6123 L22: 1.8019 REMARK 3 L33: 0.9693 L12: -0.0710 REMARK 3 L13: 0.0513 L23: 0.0783 REMARK 3 S TENSOR REMARK 3 S11: -0.0293 S12: 0.5041 S13: 0.0393 REMARK 3 S21: -0.6145 S22: 0.3559 S23: -0.6067 REMARK 3 S31: -0.3696 S32: 0.5205 S33: 0.0024 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 330:386 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.735 20.294 0.760 REMARK 3 T TENSOR REMARK 3 T11: 0.1338 T22: 0.1432 REMARK 3 T33: 0.1372 T12: 0.0017 REMARK 3 T13: -0.0086 T23: -0.0353 REMARK 3 L TENSOR REMARK 3 L11: 1.8580 L22: 1.8808 REMARK 3 L33: 1.2116 L12: 0.2463 REMARK 3 L13: -0.0300 L23: 0.0540 REMARK 3 S TENSOR REMARK 3 S11: -0.0552 S12: -0.2470 S13: 0.1703 REMARK 3 S21: 0.0645 S22: 0.1069 S23: -0.0342 REMARK 3 S31: -0.0398 S32: -0.0982 S33: 3.8447 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 387:495 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.448 -5.078 -7.455 REMARK 3 T TENSOR REMARK 3 T11: 0.1795 T22: 0.1181 REMARK 3 T33: 0.2503 T12: -0.0218 REMARK 3 T13: -0.0200 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 1.3365 L22: 1.1315 REMARK 3 L33: 2.2463 L12: -0.4817 REMARK 3 L13: 0.6936 L23: -0.1617 REMARK 3 S TENSOR REMARK 3 S11: 0.1145 S12: -0.0663 S13: -0.4540 REMARK 3 S21: 0.0400 S22: 0.0244 S23: 0.0054 REMARK 3 S31: 0.2928 S32: -0.0034 S33: 0.0190 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 496:575 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.684 1.878 -27.729 REMARK 3 T TENSOR REMARK 3 T11: 0.2673 T22: 0.2886 REMARK 3 T33: 0.1802 T12: 0.0022 REMARK 3 T13: -0.0148 T23: -0.0632 REMARK 3 L TENSOR REMARK 3 L11: 1.0058 L22: 1.8566 REMARK 3 L33: 2.3215 L12: -0.6500 REMARK 3 L13: 0.3523 L23: 0.0612 REMARK 3 S TENSOR REMARK 3 S11: 0.0765 S12: 0.4929 S13: -0.0592 REMARK 3 S21: -0.4001 S22: -0.0195 S23: 0.0911 REMARK 3 S31: -0.0639 S32: 0.1073 S33: 0.0069 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN T AND RESID 1:11 ) OR ( CHAIN P AND RESID REMARK 3 1:6 ) OR ( CHAIN D AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.712 15.534 -16.993 REMARK 3 T TENSOR REMARK 3 T11: 0.1745 T22: 0.1622 REMARK 3 T33: 0.1442 T12: 0.0146 REMARK 3 T13: -0.0101 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.6078 L22: 0.5795 REMARK 3 L33: 1.1911 L12: 0.1777 REMARK 3 L13: -0.1925 L23: 0.8065 REMARK 3 S TENSOR REMARK 3 S11: 0.0058 S12: 0.2693 S13: 0.1051 REMARK 3 S21: -0.1838 S22: 0.0240 S23: 0.1641 REMARK 3 S31: -0.1752 S32: -0.1712 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 9NPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1000293902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-25 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9202 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60232 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 41.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 1.54100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 68 MM NA CACODYLATE PH 6.5, 20.4% REMARK 280 (W/V) PEG8000, 136 MM AMMONIUM SULFATE, 12% (V/V) GLYCEROL, REMARK 280 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 28.10200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.04800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.96150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.04800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.10200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.96150 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: 5920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17020 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 230 REMARK 465 SER A 231 REMARK 465 ALA A 232 REMARK 465 ALA A 233 REMARK 465 ALA A 234 REMARK 465 VAL A 235 REMARK 465 LEU A 236 REMARK 465 ASP A 237 REMARK 465 LYS A 238 REMARK 465 VAL A 537 REMARK 465 ARG A 538 REMARK 465 ASN A 539 REMARK 465 THR A 540 REMARK 465 HIS A 541 REMARK 465 GLY A 542 REMARK 465 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 465 GLY A 546 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 VAL A 240 CG1 CG2 REMARK 470 GLN A 243 CG CD OE1 NE2 REMARK 470 GLN A 247 CG CD OE1 NE2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 THR A 250 OG1 CG2 REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 259 CE NZ REMARK 470 LYS A 265 CD CE NZ REMARK 470 LYS A 273 CE NZ REMARK 470 PHE A 289 CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CD CE NZ REMARK 470 ARG A 308 CD NE CZ NH1 NH2 REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 ILE A 316 CG1 CG2 CD1 REMARK 470 LEU A 317 CD1 CD2 REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 HIS A 321 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 324 CD CE NZ REMARK 470 GLU A 385 CD OE1 OE2 REMARK 470 GLU A 390 CD OE1 OE2 REMARK 470 LEU A 411 CD1 CD2 REMARK 470 ARG A 438 CD NE CZ NH1 NH2 REMARK 470 ARG A 441 CD NE CZ NH1 NH2 REMARK 470 ARG A 446 CZ NH1 NH2 REMARK 470 ASP A 449 CG OD1 OD2 REMARK 470 GLN A 453 CD OE1 NE2 REMARK 470 GLU A 466 CG CD OE1 OE2 REMARK 470 LYS A 523 NZ REMARK 470 LYS A 557 CE NZ REMARK 470 ARG A 568 NE CZ NH1 NH2 REMARK 470 GLU A 569 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 DT T 7 O3' DT T 7 C3' -0.045 REMARK 500 DA P 2 O4' DA P 2 C4' 0.056 REMARK 500 DT P 4 C4 DT P 4 O4 0.056 REMARK 500 DT P 4 C5 DT P 4 C7 -0.059 REMARK 500 DC P 6 O3' DC P 6 C3' 0.090 REMARK 500 DG D 1 P DG D 1 OP3 -0.120 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 DG T 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT T 7 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DT T 10 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC P 1 O4' - C1' - C2' ANGL. DEV. = 3.3 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 CYS A 415 -138.29 -114.28 REMARK 500 ARG A 438 -15.97 -142.64 REMARK 500 SER A 463 97.40 -164.34 REMARK 500 SER A 463 99.75 -164.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH P 131 DISTANCE = 6.24 ANGSTROMS 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 607 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 101.8 REMARK 620 3 ALA A 344 O 88.4 87.1 REMARK 620 4 HOH A 859 O 90.4 94.5 178.1 REMARK 620 5 DA P 5 OP1 162.0 95.9 89.3 91.4 REMARK 620 6 HOH P 105 O 73.6 171.5 85.7 92.7 88.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 605 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD1 88.2 REMARK 620 3 ASP A 490 OD2 93.1 98.8 REMARK 620 4 DUP A 604 O1A 96.8 89.3 167.4 REMARK 620 5 HOH A 752 O 87.1 169.6 90.6 82.1 REMARK 620 6 DC P 6 O3' 163.6 98.8 71.2 98.1 88.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 606 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 90.9 REMARK 620 3 DUP A 604 O1A 95.6 89.3 REMARK 620 4 DUP A 604 O2B 171.0 92.4 92.8 REMARK 620 5 DUP A 604 O1G 89.1 177.9 92.8 87.3 REMARK 620 6 HOH A 764 O 83.6 84.2 173.4 88.4 93.7 REMARK 620 N 1 2 3 4 5 DBREF 9NPU A 234 575 UNP Q9UGP5 DPOLL_HUMAN 234 575 DBREF 9NPU T 1 11 PDB 9NPU 9NPU 1 11 DBREF 9NPU P 1 6 PDB 9NPU 9NPU 1 6 DBREF 9NPU D 1 4 PDB 9NPU 9NPU 1 4 SEQADV 9NPU GLY A 230 UNP Q9UGP5 EXPRESSION TAG SEQADV 9NPU SER A 231 UNP Q9UGP5 EXPRESSION TAG SEQADV 9NPU ALA A 232 UNP Q9UGP5 EXPRESSION TAG SEQADV 9NPU ALA A 233 UNP Q9UGP5 EXPRESSION TAG SEQRES 1 A 346 GLY SER ALA ALA ALA VAL LEU ASP LYS TRP VAL CYS ALA SEQRES 2 A 346 GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU HIS SEQRES 3 A 346 ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SER SEQRES 4 A 346 VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA LYS SEQRES 5 A 346 ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL THR SEQRES 6 A 346 SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY LYS SEQRES 7 A 346 ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER GLY SEQRES 8 A 346 HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL PRO SEQRES 9 A 346 VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY THR SEQRES 10 A 346 LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SER SEQRES 11 A 346 LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR GLN SEQRES 12 A 346 GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU GLU SEQRES 13 A 346 ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN THR SEQRES 14 A 346 VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU LEU SEQRES 15 A 346 CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA THR SEQRES 16 A 346 CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP GLY SEQRES 17 A 346 ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SER SEQRES 18 A 346 LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SER SEQRES 19 A 346 GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU GLY VAL SEQRES 20 A 346 CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG ARG LEU SEQRES 21 A 346 ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA CYS ALA SEQRES 22 A 346 LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN ARG SER SEQRES 23 A 346 MET ARG ALA LEU ALA LYS THR LYS GLY MET SER LEU SER SEQRES 24 A 346 GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN THR HIS SEQRES 25 A 346 GLY CYS LYS VAL GLY PRO GLY ARG VAL LEU PRO THR PRO SEQRES 26 A 346 THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU PRO TYR SEQRES 27 A 346 ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 T 11 DC DG DG DC DA G DT DA DC DT DG SEQRES 1 P 6 DC DA DG DT DA DC SEQRES 1 D 4 DG DC DC DG HET SO4 A 601 5 HET SO4 A 602 5 HET GOL A 603 14 HET DUP A 604 37 HET MG A 605 1 HET MG A 606 1 HET NA A 607 1 HET CL A 608 1 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 GOL C3 H8 O3 FORMUL 8 DUP C9 H16 N3 O13 P3 FORMUL 9 MG 2(MG 2+) FORMUL 11 NA NA 1+ FORMUL 12 CL CL 1- FORMUL 13 HOH *265(H2 O) HELIX 1 AA1 TRP A 239 GLN A 243 5 5 HELIX 2 AA2 PRO A 244 ALA A 249 5 6 HELIX 3 AA3 ASN A 253 GLN A 270 1 18 HELIX 4 AA4 ASP A 272 PHE A 289 1 18 HELIX 5 AA5 SER A 295 ILE A 302 1 8 HELIX 6 AA6 GLY A 306 GLY A 320 1 15 HELIX 7 AA7 LEU A 322 ILE A 328 5 7 HELIX 8 AA8 SER A 331 ASN A 340 1 10 HELIX 9 AA9 GLY A 345 GLN A 355 1 11 HELIX 10 AB1 SER A 359 ALA A 367 1 9 HELIX 11 AB2 THR A 370 HIS A 379 1 10 HELIX 12 AB3 HIS A 379 GLU A 385 1 7 HELIX 13 AB4 ARG A 389 ASN A 407 1 19 HELIX 14 AB5 CYS A 415 ARG A 420 1 6 HELIX 15 AB6 GLY A 442 GLU A 454 1 13 HELIX 16 AB7 PRO A 495 SER A 497 5 3 HELIX 17 AB8 GLU A 498 GLY A 508 1 11 HELIX 18 AB9 SER A 509 LYS A 523 1 15 HELIX 19 AC1 THR A 555 LEU A 563 1 9 HELIX 20 AC2 GLU A 569 ASP A 574 5 6 SHEET 1 AA1 2 MET A 387 PRO A 388 0 SHEET 2 AA1 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 AA2 5 LEU A 411 ALA A 414 0 SHEET 2 AA2 5 ASP A 427 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 AA2 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N GLY A 475 O LEU A 489 SHEET 5 AA2 5 LEU A 457 VAL A 462 -1 N VAL A 462 O LEU A 474 SHEET 1 AA3 2 MET A 525 LEU A 527 0 SHEET 2 AA3 2 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 LINK O SER A 339 NA NA A 607 1555 1555 2.28 LINK O ILE A 341 NA NA A 607 1555 1555 2.42 LINK O ALA A 344 NA NA A 607 1555 1555 2.27 LINK OD2 ASP A 427 MG MG A 605 1555 1555 1.95 LINK OD1 ASP A 427 MG MG A 606 1555 1555 2.03 LINK OD1 ASP A 429 MG MG A 605 1555 1555 2.11 LINK OD2 ASP A 429 MG MG A 606 1555 1555 2.11 LINK OD2 ASP A 490 MG MG A 605 1555 1555 2.11 LINK O1A DUP A 604 MG MG A 605 1555 1555 2.26 LINK O1A DUP A 604 MG MG A 606 1555 1555 2.06 LINK O2B DUP A 604 MG MG A 606 1555 1555 2.04 LINK O1G DUP A 604 MG MG A 606 1555 1555 2.00 LINK MG MG A 605 O HOH A 752 1555 1555 2.29 LINK MG MG A 605 O3'A DC P 6 1555 1555 2.34 LINK MG MG A 606 O HOH A 764 1555 1555 2.22 LINK NA NA A 607 O HOH A 859 1555 1555 2.42 LINK NA NA A 607 OP1 DA P 5 1555 1555 2.44 LINK NA NA A 607 O HOH P 105 1555 1555 2.72 CISPEP 1 GLY A 508 SER A 509 0 4.06 CRYST1 56.204 59.923 140.096 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 0.017792 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007138 0.00000 CONECT 1377 5689 CONECT 1402 5689 CONECT 1452 5689 CONECT 2755 5688 CONECT 2756 5687 CONECT 2783 5687 CONECT 2784 5688 CONECT 3751 5687 CONECT 5403 5689 CONECT 5450 5687 CONECT 5626 5627 5628 5629 5630 CONECT 5627 5626 CONECT 5628 5626 CONECT 5629 5626 CONECT 5630 5626 CONECT 5631 5632 5633 5634 5635 CONECT 5632 5631 CONECT 5633 5631 CONECT 5634 5631 CONECT 5635 5631 CONECT 5636 5637 5638 5642 5643 CONECT 5637 5636 5644 CONECT 5638 5636 5639 5640 5645 CONECT 5639 5638 5646 CONECT 5640 5638 5641 5647 5648 CONECT 5641 5640 5649 CONECT 5642 5636 CONECT 5643 5636 CONECT 5644 5637 CONECT 5645 5638 CONECT 5646 5639 CONECT 5647 5640 CONECT 5648 5640 CONECT 5649 5641 CONECT 5650 5651 CONECT 5651 5650 5652 5654 CONECT 5652 5651 5653 CONECT 5653 5652 5657 CONECT 5654 5651 5655 CONECT 5655 5654 5656 5657 CONECT 5656 5655 CONECT 5657 5653 5655 5658 CONECT 5658 5657 5659 5662 5678 CONECT 5659 5658 5660 5679 5680 CONECT 5660 5659 5661 5663 5681 CONECT 5661 5660 5682 CONECT 5662 5658 5663 CONECT 5663 5660 5662 5664 5683 CONECT 5664 5663 5665 5684 5685 CONECT 5665 5664 5666 CONECT 5666 5665 5667 5668 5669 CONECT 5667 5666 5687 5688 CONECT 5668 5666 CONECT 5669 5666 5670 5686 CONECT 5670 5669 5671 5672 5673 CONECT 5671 5670 CONECT 5672 5670 5688 CONECT 5673 5670 5674 CONECT 5674 5673 5675 5676 5677 CONECT 5675 5674 CONECT 5676 5674 5688 CONECT 5677 5674 CONECT 5678 5658 CONECT 5679 5659 CONECT 5680 5659 CONECT 5681 5660 CONECT 5682 5661 CONECT 5683 5663 CONECT 5684 5664 CONECT 5685 5664 CONECT 5686 5669 CONECT 5687 2756 2783 3751 5450 CONECT 5687 5667 5743 CONECT 5688 2755 2784 5667 5672 CONECT 5688 5676 5755 CONECT 5689 1377 1402 1452 5403 CONECT 5689 5850 5928 CONECT 5743 5687 CONECT 5755 5688 CONECT 5850 5689 CONECT 5928 5689 MASTER 475 0 8 20 9 0 0 6 3203 4 81 30 END