HEADER TRANSFERASE 10-MAR-21 7M07 TITLE PRE-CATALYTIC TERNARY COMPLEX OF DNA POLYMERASE LAMBDA WITH BOUND 1-NT TITLE 2 GAPPED SSB SUBSTRATE 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 (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*C)-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: 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 NONHOMOLOGOUS END-JOINING, BASE EXCISION REPAIR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.KAMINSKI,K.BEBENEK,L.C.PEDERSEN,T.A.KUNKEL REVDAT 3 25-OCT-23 7M07 1 REMARK REVDAT 2 15-FEB-23 7M07 1 JRNL REVDAT 1 16-MAR-22 7M07 0 JRNL AUTH A.M.KAMINSKI,K.K.CHIRUVELLA,D.A.RAMSDEN,K.BEBENEK, JRNL AUTH 2 T.A.KUNKEL,L.C.PEDERSEN JRNL TITL ANALYSIS OF DIVERSE DOUBLE-STRAND BREAK SYNAPSIS WITH POL JRNL TITL 2 LAMBDA REVEALS BASIS FOR UNIQUE SUBSTRATE SPECIFICITY IN JRNL TITL 3 NONHOMOLOGOUS END-JOINING. JRNL REF NAT COMMUN V. 13 3806 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35778389 JRNL DOI 10.1038/S41467-022-31278-4 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 65909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3298 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 45.3600 - 4.5300 0.99 2815 146 0.1797 0.1779 REMARK 3 2 4.5300 - 3.6000 1.00 2695 142 0.1491 0.1486 REMARK 3 3 3.6000 - 3.1400 1.00 2650 140 0.1664 0.1825 REMARK 3 4 3.1400 - 2.8500 1.00 2653 145 0.1747 0.1805 REMARK 3 5 2.8500 - 2.6500 1.00 2638 130 0.1788 0.1806 REMARK 3 6 2.6500 - 2.4900 1.00 2606 142 0.1695 0.1835 REMARK 3 7 2.4900 - 2.3700 1.00 2631 135 0.1714 0.1934 REMARK 3 8 2.3700 - 2.2700 1.00 2604 136 0.1754 0.2165 REMARK 3 9 2.2700 - 2.1800 1.00 2626 141 0.1699 0.2014 REMARK 3 10 2.1800 - 2.1000 1.00 2609 130 0.1715 0.2050 REMARK 3 11 2.1000 - 2.0400 1.00 2595 152 0.1677 0.2175 REMARK 3 12 2.0400 - 1.9800 1.00 2577 125 0.1689 0.2081 REMARK 3 13 1.9800 - 1.9300 1.00 2592 138 0.1632 0.1772 REMARK 3 14 1.9300 - 1.8800 1.00 2596 141 0.1628 0.1854 REMARK 3 15 1.8800 - 1.8400 1.00 2594 137 0.1699 0.2373 REMARK 3 16 1.8400 - 1.8000 1.00 2575 142 0.1824 0.2172 REMARK 3 17 1.8000 - 1.7600 1.00 2571 126 0.1945 0.2328 REMARK 3 18 1.7600 - 1.7300 1.00 2637 122 0.1817 0.2157 REMARK 3 19 1.7300 - 1.7000 1.00 2525 165 0.1618 0.1758 REMARK 3 20 1.7000 - 1.6700 1.00 2556 122 0.1663 0.2213 REMARK 3 21 1.6700 - 1.6400 1.00 2609 144 0.1741 0.1864 REMARK 3 22 1.6400 - 1.6200 1.00 2578 144 0.1754 0.2093 REMARK 3 23 1.6200 - 1.5900 1.00 2598 120 0.1901 0.2343 REMARK 3 24 1.5900 - 1.5700 0.98 2481 133 0.2175 0.2347 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) : 0.146 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.055 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.72 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 : 0.010 3171 REMARK 3 ANGLE : 0.986 4401 REMARK 3 CHIRALITY : 0.062 483 REMARK 3 PLANARITY : 0.008 493 REMARK 3 DIHEDRAL : 12.858 955 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): -7.7270 25.8660 -25.9756 REMARK 3 T TENSOR REMARK 3 T11: 0.3503 T22: 0.3843 REMARK 3 T33: 0.2672 T12: -0.1147 REMARK 3 T13: 0.1225 T23: -0.0783 REMARK 3 L TENSOR REMARK 3 L11: 0.3040 L22: 0.5013 REMARK 3 L33: 0.6536 L12: -0.0788 REMARK 3 L13: -0.0366 L23: -0.1802 REMARK 3 S TENSOR REMARK 3 S11: -0.0553 S12: 0.3214 S13: -0.0982 REMARK 3 S21: -0.3684 S22: 0.3445 S23: -0.3611 REMARK 3 S31: -0.1696 S32: 0.2188 S33: 0.0962 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 330:386 REMARK 3 ORIGIN FOR THE GROUP (A): -13.4696 20.0271 0.9055 REMARK 3 T TENSOR REMARK 3 T11: 0.1157 T22: 0.1239 REMARK 3 T33: 0.1335 T12: 0.0054 REMARK 3 T13: -0.0097 T23: -0.0210 REMARK 3 L TENSOR REMARK 3 L11: 0.4565 L22: 0.4334 REMARK 3 L33: 0.3385 L12: 0.1110 REMARK 3 L13: -0.0244 L23: 0.0469 REMARK 3 S TENSOR REMARK 3 S11: -0.0251 S12: -0.1059 S13: 0.0706 REMARK 3 S21: 0.0473 S22: 0.0668 S23: -0.0566 REMARK 3 S31: 0.0108 S32: -0.0599 S33: 0.0008 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 387:495 REMARK 3 ORIGIN FOR THE GROUP (A): -12.2020 -5.2633 -7.3851 REMARK 3 T TENSOR REMARK 3 T11: 0.1402 T22: 0.1165 REMARK 3 T33: 0.1971 T12: -0.0083 REMARK 3 T13: -0.0233 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 0.4093 L22: 0.3530 REMARK 3 L33: 1.0131 L12: -0.2407 REMARK 3 L13: 0.2374 L23: -0.1136 REMARK 3 S TENSOR REMARK 3 S11: 0.0672 S12: -0.0025 S13: -0.2188 REMARK 3 S21: 0.0179 S22: 0.0204 S23: 0.0110 REMARK 3 S31: 0.1345 S32: 0.0617 S33: 0.0029 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 496:575 REMARK 3 ORIGIN FOR THE GROUP (A): -19.3357 1.7070 -27.7299 REMARK 3 T TENSOR REMARK 3 T11: 0.2167 T22: 0.2065 REMARK 3 T33: 0.1321 T12: 0.0195 REMARK 3 T13: -0.0206 T23: -0.0372 REMARK 3 L TENSOR REMARK 3 L11: 0.3115 L22: 0.3106 REMARK 3 L33: 0.5415 L12: -0.0530 REMARK 3 L13: -0.0219 L23: 0.0932 REMARK 3 S TENSOR REMARK 3 S11: 0.0272 S12: 0.2398 S13: -0.0601 REMARK 3 S21: -0.2197 S22: -0.0040 S23: 0.0194 REMARK 3 S31: -0.0876 S32: 0.0976 S33: 0.0109 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -25.4643 16.6530 -18.0390 REMARK 3 T TENSOR REMARK 3 T11: 0.1367 T22: 0.1685 REMARK 3 T33: 0.1375 T12: 0.0210 REMARK 3 T13: -0.0278 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.2451 L22: 0.3788 REMARK 3 L33: 0.4106 L12: 0.0156 REMARK 3 L13: -0.1248 L23: 0.4162 REMARK 3 S TENSOR REMARK 3 S11: 0.0063 S12: 0.1104 S13: 0.0179 REMARK 3 S21: -0.0946 S22: -0.0182 S23: 0.1998 REMARK 3 S31: -0.0673 S32: -0.1049 S33: -0.0340 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 7M07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-20 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(III) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65998 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 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 : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50000 REMARK 200 FOR SHELL : 1.750 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: 2PFO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 37.5MM NA CACODYLATE PH 6.5, 150MM REMARK 280 KCL, 75MM MAGNESIUM ACETATE, 7.5% (W/V) PEG 8000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 28.00150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.82450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.83250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.82450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.00150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.83250 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: 6850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -112.0 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 LYS A 248 CG CD CE NZ REMARK 470 THR A 250 OG1 CG2 REMARK 470 LEU A 254 CD1 CD2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 261 CG CD OE1 OE2 REMARK 470 LYS A 265 CD CE NZ REMARK 470 LYS A 273 CD CE NZ REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CG 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 HIS A 321 ND1 CD2 CE1 NE2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 324 CE NZ 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 CG 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 GLU A 569 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 802 O HOH A 964 2.19 REMARK 500 O HOH A 1094 O HOH A 1116 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 -0.114 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. = 2.5 DEGREES REMARK 500 DG T 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 1.9 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 CYS A 415 -139.00 -110.96 REMARK 500 ARG A 438 -24.94 -141.65 REMARK 500 SER A 463 94.87 -164.93 REMARK 500 SER A 463 96.95 -164.93 REMARK 500 ASP A 574 59.70 -91.60 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 A1120 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A1121 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH P 136 DISTANCE = 6.25 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 706 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 247 O REMARK 620 2 THR A 250 O 94.5 REMARK 620 3 LYS A 287 O 79.0 86.2 REMARK 620 4 SER A 288 O 85.6 172.6 86.5 REMARK 620 5 PHE A 289 O 144.5 119.9 93.9 59.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 705 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 O REMARK 620 2 ILE A 302 O 88.9 REMARK 620 3 ILE A 305 O 84.7 77.3 REMARK 620 4 HOH A1030 O 89.3 79.5 156.1 REMARK 620 5 DC D 3 OP1 172.5 84.6 90.2 93.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 704 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 99.6 REMARK 620 3 ALA A 344 O 88.0 84.3 REMARK 620 4 HOH A1052 O 90.9 99.2 176.5 REMARK 620 5 DA P 5 OP1 164.8 95.1 89.6 90.6 REMARK 620 6 HOH P 103 O 74.8 166.5 83.2 93.3 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD1 97.7 REMARK 620 3 ASP A 490 OD2 89.4 97.9 REMARK 620 4 DUP A 701 O2A 97.8 89.0 169.3 REMARK 620 5 HOH A 892 O 84.4 171.2 90.6 82.3 REMARK 620 6 DC P 6 O3' 162.7 92.1 75.1 96.6 88.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 93.6 REMARK 620 3 DUP A 701 O2A 95.6 89.2 REMARK 620 4 DUP A 701 O2B 171.2 91.8 91.4 REMARK 620 5 DUP A 701 O3G 87.3 179.1 90.5 87.4 REMARK 620 6 HOH A 909 O 83.9 87.9 177.1 89.3 92.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 708 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 463 O REMARK 620 2 HOH A1023 O 82.2 REMARK 620 3 HOH A1094 O 117.4 107.2 REMARK 620 4 HOH A1116 O 167.4 101.9 49.9 REMARK 620 5 HOH T 208 O 89.7 65.4 151.4 102.9 REMARK 620 6 HOH T 216 O 102.5 150.0 96.9 80.1 84.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA T 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1103 O REMARK 620 2 DC T 4 OP2 123.3 REMARK 620 3 DC T 4 O5' 143.1 51.1 REMARK 620 4 HOH T 254 O 80.1 119.9 136.4 REMARK 620 N 1 2 3 DBREF 7M07 A 234 575 UNP Q9UGP5 DPOLL_HUMAN 234 575 DBREF 7M07 T 1 11 PDB 7M07 7M07 1 11 DBREF 7M07 P 1 6 PDB 7M07 7M07 1 6 DBREF 7M07 D 1 4 PDB 7M07 7M07 1 4 SEQADV 7M07 GLY A 230 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M07 SER A 231 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M07 ALA A 232 UNP Q9UGP5 EXPRESSION TAG SEQADV 7M07 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 DG DT DA DC DT DG SEQRES 1 P 6 DC DA DG DT DA DC SEQRES 1 D 4 DG DC DC DG HET DUP A 701 28 HET MG A 702 1 HET MG A 703 1 HET NA A 704 1 HET NA A 705 1 HET NA A 706 1 HET CL A 707 1 HET NA A 708 1 HET CL A 709 1 HET EDO A 710 4 HET EDO A 711 4 HET EDO A 712 4 HET NA T 101 1 HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 DUP C9 H16 N3 O13 P3 FORMUL 6 MG 2(MG 2+) FORMUL 8 NA 5(NA 1+) FORMUL 11 CL 2(CL 1-) FORMUL 14 EDO 3(C2 H6 O2) FORMUL 18 HOH *427(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 GLY A 271 1 19 HELIX 4 AA4 ASP A 272 PHE A 289 1 18 HELIX 5 AA5 SER A 295 SER A 301 1 7 HELIX 6 AA6 GLY A 306 GLY A 320 1 15 HELIX 7 AA7 LEU A 322 HIS A 327 5 6 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 CYS A 477 O ARG A 487 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 GLN A 247 NA NA A 706 1555 1555 2.60 LINK O THR A 250 NA NA A 706 1555 1555 2.52 LINK O LYS A 287 NA NA A 706 1555 1555 2.84 LINK O SER A 288 NA NA A 706 1555 1555 3.07 LINK O PHE A 289 NA NA A 706 1555 1555 2.92 LINK O CYS A 300 NA NA A 705 1555 1555 2.55 LINK O ILE A 302 NA NA A 705 1555 1555 2.70 LINK O ILE A 305 NA NA A 705 1555 1555 2.69 LINK O SER A 339 NA NA A 704 1555 1555 2.31 LINK O ILE A 341 NA NA A 704 1555 1555 2.51 LINK O ALA A 344 NA NA A 704 1555 1555 2.36 LINK OD2 ASP A 427 MG MG A 702 1555 1555 1.98 LINK OD1 ASP A 427 MG MG A 703 1555 1555 2.05 LINK OD1 ASP A 429 MG MG A 702 1555 1555 2.04 LINK OD2 ASP A 429 MG MG A 703 1555 1555 2.05 LINK O SER A 463 NA NA A 708 1555 1555 2.45 LINK OD2 ASP A 490 MG MG A 702 1555 1555 2.06 LINK O2A DUP A 701 MG MG A 702 1555 1555 2.26 LINK O2A DUP A 701 MG MG A 703 1555 1555 2.11 LINK O2B DUP A 701 MG MG A 703 1555 1555 2.05 LINK O3G DUP A 701 MG MG A 703 1555 1555 2.09 LINK MG MG A 702 O HOH A 892 1555 1555 2.10 LINK MG MG A 702 O3' DC P 6 1555 1555 2.27 LINK MG MG A 703 O HOH A 909 1555 1555 2.18 LINK NA NA A 704 O HOH A1052 1555 1555 2.34 LINK NA NA A 704 OP1 DA P 5 1555 1555 2.39 LINK NA NA A 704 O HOH P 103 1555 1555 2.71 LINK NA NA A 705 O HOH A1030 1555 1555 2.80 LINK NA NA A 705 OP1 DC D 3 1555 1555 2.92 LINK NA NA A 708 O HOH A1023 1555 1555 2.59 LINK NA NA A 708 O HOH A1094 1555 1555 2.56 LINK NA NA A 708 O HOH A1116 1555 1555 2.63 LINK NA NA A 708 O HOH T 208 1555 1555 3.00 LINK NA NA A 708 O HOH T 216 1555 1555 2.96 LINK O HOH A1103 NA NA T 101 1555 1555 2.78 LINK OP2 DC T 4 NA NA T 101 1555 1555 2.69 LINK O5' DC T 4 NA NA T 101 1555 1555 3.01 LINK NA NA T 101 O HOH T 254 1555 1555 2.93 CISPEP 1 GLY A 508 SER A 509 0 3.41 CRYST1 56.003 59.665 139.649 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 0.017856 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016760 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007161 0.00000