HEADER REPLICATION 29-AUG-25 9Y1E TITLE S180R HUMAN DNA POLYMERASE BETA, BINARY COMPLEX TEMPLATING DG COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5'-DEOXYRIBOSE-PHOSPHATE LYASE,5'-DRP LYASE,AP LYASE; COMPND 5 EC: 2.7.7.7,4.2.99.-,4.2.99.18; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TEMPLATE STRAND; COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: PRIMER STRAND; COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DOWNSTREAM; 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: POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630 KEYWDS POLYMERASE, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR B.E.ECKENROTH,S.DOUBLIE REVDAT 1 28-JAN-26 9Y1E 0 JRNL AUTH D.L.SAWYER,B.E.ECKENROTH,C.CHAVIRA,K.ALNAJJAR,J.P.HANLEY, JRNL AUTH 2 J.A.DRAGON,S.DOUBLIE,J.B.SWEASY JRNL TITL THE S180R HUMAN GERMLINE VARIANT OF DNA POLYMERASE BETA IS A JRNL TITL 2 LOW FIDELITY ENZYME WITH REDUCED FLEXIBILITY OF THE FINGERS JRNL TITL 3 DOMAIN. JRNL REF BIOCHEMISTRY 2026 JRNL REFN ISSN 0006-2960 JRNL PMID 41524291 JRNL DOI 10.1021/ACS.BIOCHEM.5C00628 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 114653 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.790 REMARK 3 FREE R VALUE TEST SET COUNT : 11220 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 43.6100 - 4.9800 0.99 3462 375 0.1415 0.1445 REMARK 3 2 4.9800 - 3.9600 0.99 3445 411 0.1290 0.1468 REMARK 3 3 3.9500 - 3.4600 0.99 3481 337 0.1466 0.1814 REMARK 3 4 3.4600 - 3.1400 0.99 3474 408 0.1585 0.1857 REMARK 3 5 3.1400 - 2.9100 0.99 3437 429 0.1834 0.1898 REMARK 3 6 2.9100 - 2.7400 0.99 3434 412 0.1840 0.2169 REMARK 3 7 2.7400 - 2.6100 0.99 3458 397 0.1814 0.2119 REMARK 3 8 2.6100 - 2.4900 0.99 3452 409 0.1832 0.2227 REMARK 3 9 2.4900 - 2.4000 1.00 3605 329 0.1855 0.2434 REMARK 3 10 2.4000 - 2.3100 0.99 3451 403 0.1852 0.2132 REMARK 3 11 2.3100 - 2.2400 1.00 3475 413 0.1781 0.2011 REMARK 3 12 2.2400 - 2.1800 0.99 3463 374 0.1799 0.2072 REMARK 3 13 2.1800 - 2.1200 1.00 3507 396 0.1757 0.2228 REMARK 3 14 2.1200 - 2.0700 0.99 3501 383 0.1970 0.2348 REMARK 3 15 2.0700 - 2.0200 1.00 3447 381 0.2256 0.2548 REMARK 3 16 2.0200 - 1.9800 1.00 3482 397 0.2241 0.2394 REMARK 3 17 1.9800 - 1.9400 1.00 3506 350 0.2168 0.2304 REMARK 3 18 1.9400 - 1.9000 1.00 3541 361 0.2059 0.2489 REMARK 3 19 1.9000 - 1.8700 1.00 3592 326 0.2082 0.2403 REMARK 3 20 1.8700 - 1.8400 0.99 3488 337 0.2084 0.2534 REMARK 3 21 1.8400 - 1.8100 1.00 3519 405 0.2202 0.2490 REMARK 3 22 1.8100 - 1.7800 1.00 3475 365 0.2399 0.2769 REMARK 3 23 1.7800 - 1.7500 1.00 3472 387 0.2537 0.2929 REMARK 3 24 1.7500 - 1.7300 1.00 3520 332 0.2772 0.3184 REMARK 3 25 1.7300 - 1.7000 0.99 3517 380 0.2998 0.3297 REMARK 3 26 1.7000 - 1.6800 0.99 3447 396 0.3291 0.3385 REMARK 3 27 1.6800 - 1.6600 0.98 3389 370 0.3391 0.3622 REMARK 3 28 1.6600 - 1.6400 0.96 3408 335 0.3527 0.3659 REMARK 3 29 1.6400 - 1.6200 0.94 3285 395 0.3778 0.4374 REMARK 3 30 1.6200 - 1.6000 0.75 2700 227 0.4133 0.4147 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.10 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 : 0.007 3382 REMARK 3 ANGLE : 0.903 4696 REMARK 3 CHIRALITY : 0.052 520 REMARK 3 PLANARITY : 0.009 498 REMARK 3 DIHEDRAL : 19.355 1334 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ((CHAIN D AND RESID 1:5) OR (CHAIN T AND RESID 1:5)) REMARK 3 ORIGIN FOR THE GROUP (A): 31.8978 9.5202 -3.3938 REMARK 3 T TENSOR REMARK 3 T11: 0.3448 T22: 0.2475 REMARK 3 T33: 0.1826 T12: 0.0353 REMARK 3 T13: 0.0140 T23: 0.0258 REMARK 3 L TENSOR REMARK 3 L11: 1.7280 L22: 2.1263 REMARK 3 L33: 2.2290 L12: -0.0838 REMARK 3 L13: -0.0981 L23: -0.3548 REMARK 3 S TENSOR REMARK 3 S11: 0.0771 S12: 0.3432 S13: 0.1928 REMARK 3 S21: -0.4074 S22: 0.0992 S23: -0.0472 REMARK 3 S31: 0.1374 S32: 0.0327 S33: -0.1297 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ((CHAIN P AND RESID 6:10) OR (CHAIN T AND RESID REMARK 3 7:11)) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2395 18.2115 13.9210 REMARK 3 T TENSOR REMARK 3 T11: 0.2185 T22: 0.1885 REMARK 3 T33: 0.2222 T12: -0.0109 REMARK 3 T13: 0.0226 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 1.9510 L22: 1.8314 REMARK 3 L33: 2.1420 L12: -0.5767 REMARK 3 L13: 0.0688 L23: -0.4130 REMARK 3 S TENSOR REMARK 3 S11: 0.0308 S12: 0.1866 S13: 0.0163 REMARK 3 S21: -0.1938 S22: -0.0790 S23: -0.1840 REMARK 3 S31: -0.1279 S32: 0.0616 S33: 0.0460 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 12:90 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0710 -4.3353 9.5403 REMARK 3 T TENSOR REMARK 3 T11: 0.1977 T22: 0.1549 REMARK 3 T33: 0.1734 T12: -0.0294 REMARK 3 T13: -0.0007 T23: 0.0094 REMARK 3 L TENSOR REMARK 3 L11: 1.6556 L22: 2.9572 REMARK 3 L33: 2.1734 L12: -0.2240 REMARK 3 L13: 0.0781 L23: 0.5360 REMARK 3 S TENSOR REMARK 3 S11: 0.0253 S12: -0.0501 S13: -0.1994 REMARK 3 S21: -0.1045 S22: -0.0201 S23: -0.0359 REMARK 3 S31: 0.2175 S32: -0.2084 S33: -0.0178 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 21.7967 9.6936 29.0653 REMARK 3 T TENSOR REMARK 3 T11: 0.1306 T22: 0.1980 REMARK 3 T33: 0.1508 T12: -0.0112 REMARK 3 T13: -0.0057 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 3.5749 L22: 1.4378 REMARK 3 L33: 1.5693 L12: -0.8835 REMARK 3 L13: -0.0971 L23: 0.0517 REMARK 3 S TENSOR REMARK 3 S11: 0.0367 S12: -0.5273 S13: -0.0769 REMARK 3 S21: 0.0912 S22: 0.0404 S23: -0.0538 REMARK 3 S31: -0.0247 S32: 0.1481 S33: -0.0743 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -2.1546 7.8683 18.6316 REMARK 3 T TENSOR REMARK 3 T11: 0.1136 T22: 0.1540 REMARK 3 T33: 0.1784 T12: -0.0134 REMARK 3 T13: 0.0119 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 3.9454 L22: 2.7185 REMARK 3 L33: 2.0880 L12: 0.4579 REMARK 3 L13: 0.5172 L23: 0.3161 REMARK 3 S TENSOR REMARK 3 S11: 0.0618 S12: -0.0781 S13: -0.1432 REMARK 3 S21: -0.0775 S22: -0.0755 S23: 0.0404 REMARK 3 S31: 0.0462 S32: -0.0997 S33: 0.0143 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.7713 7.3905 -5.0383 REMARK 3 T TENSOR REMARK 3 T11: 0.5155 T22: 0.5082 REMARK 3 T33: 0.3046 T12: -0.1709 REMARK 3 T13: 0.0851 T23: -0.1531 REMARK 3 L TENSOR REMARK 3 L11: 0.7605 L22: 0.6606 REMARK 3 L33: 2.3993 L12: 0.3199 REMARK 3 L13: -0.7966 L23: -0.8432 REMARK 3 S TENSOR REMARK 3 S11: -0.4123 S12: 0.6269 S13: -0.4072 REMARK 3 S21: -0.8371 S22: 0.4367 S23: -0.2924 REMARK 3 S31: 0.2688 S32: 0.0687 S33: 0.0242 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ((CHAIN P AND RESID 1:5) OR (CHAIN T AND RESID REMARK 3 12:16)) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3403 33.2586 18.5043 REMARK 3 T TENSOR REMARK 3 T11: 0.3368 T22: 0.2271 REMARK 3 T33: 0.3684 T12: -0.0547 REMARK 3 T13: -0.0316 T23: -0.0386 REMARK 3 L TENSOR REMARK 3 L11: 2.0039 L22: 3.7200 REMARK 3 L33: 3.0877 L12: 0.3556 REMARK 3 L13: -0.2205 L23: -0.3251 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: -0.2683 S13: 0.4848 REMARK 3 S21: -0.1908 S22: -0.4307 S23: -0.4164 REMARK 3 S31: 0.0124 S32: -0.2501 S33: 0.3690 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MODEL REFINEMENT USES I+/I-. DATA REMARK 3 COLLECTION STATISTICS REPORTED FOR I-MEAN SO % COMPLETENESS AND REMARK 3 NUMBER OR REFLECTIONS MAY DIFFER BETWEEN TABLES. REMARK 4 REMARK 4 9Y1E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000299654. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 3.8 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 114653 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 43.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.88900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: CRYOPROTECTION WITH 19% PEG 3350, 150 MM SODIUM ACETATE, REMARK 200 50 MM MAGNESIUM CHLORIDE, 50 MM MAGNESIUM ACETATE, 50 MM HEPES, REMARK 200 1 MM TECP, 15% ETHYLENE GLYCOL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13-16% PEG 3350, 150-300 MM SODIUM REMARK 280 ACETATE, 50 MM HEPES, 1 MM TECP 250UM PROTEIN WITH 300 UM DNA REMARK 280 ASSEMBLY MIXED 1:1 WITH REAGENT, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.82200 REMARK 290 SMTRY3 2 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: 4130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 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 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 THR A 205 REMARK 465 LYS A 206 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 8 CG CD OE1 NE2 REMARK 470 GLU A 9 CG CD OE1 OE2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ASN A 245 CG OD1 ND2 REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 GLU A 335 CG 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 LYS A 326 O HOH A 501 1.82 REMARK 500 O HOH T 114 O HOH P 105 1.84 REMARK 500 OP2 DA T 14 O HOH T 101 1.97 REMARK 500 O HOH A 593 O HOH A 741 2.05 REMARK 500 O HOH T 102 O HOH T 162 2.09 REMARK 500 OD1 ASP A 130 O HOH A 502 2.09 REMARK 500 O HOH P 114 O HOH P 126 2.10 REMARK 500 O HOH T 119 O HOH T 170 2.10 REMARK 500 OG SER A 94 O HOH A 503 2.13 REMARK 500 O HOH A 703 O HOH A 721 2.16 REMARK 500 O HOH T 107 O HOH P 126 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 795 O HOH D 124 1556 2.12 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 T 7 O3' DG T 7 C3' -0.054 REMARK 500 DG D 1 P DG D 1 OP3 -0.124 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 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG T 15 O4' - C1' - N9 ANGL. DEV. = 1.8 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 PRO A 50 43.91 -87.67 REMARK 500 CYS A 178 -157.69 -98.95 REMARK 500 LYS A 244 46.37 -86.82 REMARK 500 ASN A 245 -13.91 64.07 REMARK 500 ASP A 246 -15.17 -142.27 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 30 O REMARK 620 2 SER A 171 OG 41.1 REMARK 620 3 HOH A 598 O 168.2 127.1 REMARK 620 4 HOH A 727 O 85.7 52.5 84.8 REMARK 620 5 HOH A 737 O 102.4 128.4 85.6 165.7 REMARK 620 6 HOH A 761 O 86.4 69.6 87.4 94.8 74.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 90.9 REMARK 620 3 VAL A 65 O 94.2 96.8 REMARK 620 4 HOH A 745 O 87.1 84.3 178.3 REMARK 620 5 DC D 3 OP1 174.7 92.6 89.4 89.3 REMARK 620 6 HOH D 116 O 91.8 171.0 91.6 87.2 84.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 92.6 REMARK 620 3 ILE A 106 O 95.0 86.6 REMARK 620 4 HOH A 748 O 83.7 95.2 177.7 REMARK 620 5 DG P 9 OP1 167.2 96.0 95.0 86.1 REMARK 620 6 HOH P 118 O 81.9 173.8 90.9 87.1 89.9 REMARK 620 N 1 2 3 4 5 DBREF 9Y1E A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1E T 1 16 PDB 9Y1E 9Y1E 1 16 DBREF 9Y1E P 1 10 PDB 9Y1E 9Y1E 1 10 DBREF 9Y1E D 1 5 PDB 9Y1E 9Y1E 1 5 SEQADV 9Y1E ARG A 180 UNP P06746 SER 180 ENGINEERED MUTATION SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY ARG PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU SEQRES 1 T 16 DC DC DG DA DC DG DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DC SEQRES 1 D 5 DG DT DC DG DG HET NA A 401 1 HET NA A 402 1 HET NA A 403 1 HET CL A 404 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 5 NA 3(NA 1+) FORMUL 8 CL CL 1- FORMUL 9 HOH *493(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 TYR A 49 1 18 HELIX 3 AA3 SER A 55 LYS A 61 1 7 HELIX 4 AA4 GLY A 66 GLY A 80 1 15 HELIX 5 AA5 LEU A 82 GLN A 90 1 9 HELIX 6 AA6 ASP A 91 THR A 101 1 11 HELIX 7 AA7 GLY A 107 GLU A 117 1 11 HELIX 8 AA8 THR A 121 LYS A 127 1 7 HELIX 9 AA9 ASN A 128 LEU A 132 5 5 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 GLU A 147 1 6 HELIX 12 AB3 ARG A 152 ASP A 170 1 19 HELIX 13 AB4 CYS A 178 ARG A 183 1 6 HELIX 14 AB5 LYS A 209 VAL A 221 1 13 HELIX 15 AB6 PRO A 261 ASP A 263 5 3 HELIX 16 AB7 GLN A 264 GLY A 274 1 11 HELIX 17 AB8 SER A 275 LYS A 289 1 15 HELIX 18 AB9 SER A 315 ILE A 323 1 9 HELIX 19 AC1 GLU A 329 ARG A 333 5 5 SHEET 1 AA1 2 ILE A 150 PRO A 151 0 SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 AA2 5 ILE A 174 VAL A 177 0 SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 AA3 2 PHE A 291 ILE A 293 0 SHEET 2 AA3 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O SER A 30 NA NA A 403 1555 1555 2.41 LINK O LYS A 60 NA NA A 401 1555 1555 2.36 LINK O LEU A 62 NA NA A 401 1555 1555 2.49 LINK O VAL A 65 NA NA A 401 1555 1555 2.27 LINK O THR A 101 NA NA A 402 1555 1555 2.29 LINK O VAL A 103 NA NA A 402 1555 1555 2.49 LINK O ILE A 106 NA NA A 402 1555 1555 2.38 LINK OG SER A 171 NA NA A 403 1555 1455 2.45 LINK NA NA A 401 O HOH A 745 1555 1555 2.47 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.89 LINK NA NA A 401 O HOH D 116 1555 1555 2.52 LINK NA NA A 402 O HOH A 748 1555 1555 2.48 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.37 LINK NA NA A 402 O HOH P 118 1555 1555 2.51 LINK NA NA A 403 O HOH A 598 1555 1655 2.51 LINK NA NA A 403 O HOH A 727 1555 1555 2.39 LINK NA NA A 403 O HOH A 737 1555 1655 2.35 LINK NA NA A 403 O HOH A 761 1555 1555 2.53 CISPEP 1 GLY A 274 SER A 275 0 0.31 CRYST1 54.494 79.644 55.013 90.00 105.60 90.00 P 1 21 1 2 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 0.018351 0.000000 0.005124 0.00000 SCALE2 0.000000 0.012556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018873 0.00000 CONECT 172 3259 CONECT 408 3257 CONECT 426 3257 CONECT 445 3257 CONECT 744 3258 CONECT 762 3258 CONECT 779 3258 CONECT 3109 3258 CONECT 3194 3257 CONECT 3257 408 426 445 3194 CONECT 3257 3505 3741 CONECT 3258 744 762 779 3109 CONECT 3258 3508 3699 CONECT 3259 172 3487 3521 CONECT 3487 3259 CONECT 3505 3257 CONECT 3508 3258 CONECT 3521 3259 CONECT 3699 3258 CONECT 3741 3257 MASTER 495 0 4 19 9 0 0 6 3719 4 20 30 END