HEADER REPLICATION 29-AUG-25 9Y1G TITLE S180R HUMAN DNA POLYMERASE BETA, BINARY COMPLEX TEMPLATING DC 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 9Y1G 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) : 43.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 113401 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.140 REMARK 3 FREE R VALUE TEST SET COUNT : 11501 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 43.8300 - 4.9800 0.98 3464 372 0.1384 0.1559 REMARK 3 2 4.9700 - 3.9500 0.98 3456 412 0.1220 0.1402 REMARK 3 3 3.9500 - 3.4500 0.98 3466 344 0.1392 0.1573 REMARK 3 4 3.4500 - 3.1400 0.99 3497 406 0.1542 0.1811 REMARK 3 5 3.1400 - 2.9100 0.99 3458 440 0.1784 0.2136 REMARK 3 6 2.9100 - 2.7400 0.99 3449 411 0.1790 0.2352 REMARK 3 7 2.7400 - 2.6000 0.99 3487 398 0.1816 0.2189 REMARK 3 8 2.6000 - 2.4900 0.99 3450 406 0.1778 0.2196 REMARK 3 9 2.4900 - 2.3900 1.00 3597 329 0.1896 0.2495 REMARK 3 10 2.3900 - 2.3100 0.99 3471 408 0.1814 0.1968 REMARK 3 11 2.3100 - 2.2400 0.99 3485 421 0.1787 0.2124 REMARK 3 12 2.2400 - 2.1700 0.99 3515 374 0.1815 0.2280 REMARK 3 13 2.1700 - 2.1200 0.99 3476 401 0.1810 0.2180 REMARK 3 14 2.1200 - 2.0700 0.99 3488 386 0.2173 0.2511 REMARK 3 15 2.0700 - 2.0200 1.00 3490 371 0.2177 0.2563 REMARK 3 16 2.0200 - 1.9800 0.99 3539 369 0.2150 0.2410 REMARK 3 17 1.9800 - 1.9400 0.99 3516 370 0.2102 0.2660 REMARK 3 18 1.9400 - 1.9000 0.99 3420 417 0.2054 0.2274 REMARK 3 19 1.9000 - 1.8700 0.99 3544 413 0.2147 0.2577 REMARK 3 20 1.8700 - 1.8300 0.99 3505 378 0.2258 0.2742 REMARK 3 21 1.8300 - 1.8000 0.99 3462 421 0.2255 0.2580 REMARK 3 22 1.8000 - 1.7800 0.99 3512 370 0.2525 0.2873 REMARK 3 23 1.7800 - 1.7500 0.99 3468 395 0.2733 0.3181 REMARK 3 24 1.7500 - 1.7300 0.99 3477 385 0.3001 0.3133 REMARK 3 25 1.7300 - 1.7000 0.98 3410 380 0.3272 0.3715 REMARK 3 26 1.7000 - 1.6800 0.95 3422 376 0.3632 0.3772 REMARK 3 27 1.6800 - 1.6600 0.92 3238 363 0.3045 0.3175 REMARK 3 28 1.6600 - 1.6400 0.87 3004 360 0.3054 0.3247 REMARK 3 29 1.6400 - 1.6200 0.80 2794 348 0.2965 0.3272 REMARK 3 30 1.6200 - 1.6000 0.66 2340 277 0.3152 0.3102 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.890 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 : 0.007 3424 REMARK 3 ANGLE : 0.893 4754 REMARK 3 CHIRALITY : 0.054 525 REMARK 3 PLANARITY : 0.009 507 REMARK 3 DIHEDRAL : 19.152 1366 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 1:6)) REMARK 3 ORIGIN FOR THE GROUP (A): 30.3516 9.6497 -2.6948 REMARK 3 T TENSOR REMARK 3 T11: 0.3084 T22: 0.2462 REMARK 3 T33: 0.1678 T12: 0.0309 REMARK 3 T13: 0.0159 T23: 0.0315 REMARK 3 L TENSOR REMARK 3 L11: 1.8071 L22: 0.8551 REMARK 3 L33: 1.6921 L12: -0.5528 REMARK 3 L13: -1.0043 L23: 0.8625 REMARK 3 S TENSOR REMARK 3 S11: 0.1865 S12: 0.4329 S13: 0.1437 REMARK 3 S21: -0.3451 S22: -0.0190 S23: -0.0083 REMARK 3 S31: 0.0328 S32: -0.0320 S33: -0.1251 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): 15.3634 18.1681 14.0887 REMARK 3 T TENSOR REMARK 3 T11: 0.1977 T22: 0.1537 REMARK 3 T33: 0.1964 T12: 0.0111 REMARK 3 T13: 0.0115 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 2.1861 L22: 2.1635 REMARK 3 L33: 2.7781 L12: -1.0756 REMARK 3 L13: -0.3440 L23: -0.1718 REMARK 3 S TENSOR REMARK 3 S11: 0.1435 S12: 0.1442 S13: 0.0770 REMARK 3 S21: -0.1677 S22: -0.1881 S23: -0.1265 REMARK 3 S31: -0.1900 S32: -0.0050 S33: 0.0609 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 12:90 REMARK 3 ORIGIN FOR THE GROUP (A): 31.8501 -4.2178 9.7906 REMARK 3 T TENSOR REMARK 3 T11: 0.1484 T22: 0.1316 REMARK 3 T33: 0.1437 T12: -0.0263 REMARK 3 T13: 0.0163 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 1.7510 L22: 3.0355 REMARK 3 L33: 3.2592 L12: 0.4178 REMARK 3 L13: 0.4092 L23: 0.5142 REMARK 3 S TENSOR REMARK 3 S11: 0.0039 S12: -0.0701 S13: -0.2337 REMARK 3 S21: -0.1417 S22: -0.0150 S23: -0.1265 REMARK 3 S31: 0.1747 S32: -0.2128 S33: -0.0005 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 91:150 REMARK 3 ORIGIN FOR THE GROUP (A): 21.7391 9.6748 29.3065 REMARK 3 T TENSOR REMARK 3 T11: 0.1164 T22: 0.1721 REMARK 3 T33: 0.1133 T12: -0.0064 REMARK 3 T13: -0.0061 T23: 0.0253 REMARK 3 L TENSOR REMARK 3 L11: 3.8677 L22: 1.9472 REMARK 3 L33: 2.0495 L12: -0.4344 REMARK 3 L13: -0.0992 L23: 0.2778 REMARK 3 S TENSOR REMARK 3 S11: 0.0245 S12: -0.5293 S13: -0.1101 REMARK 3 S21: 0.0803 S22: 0.0303 S23: -0.0957 REMARK 3 S31: -0.0186 S32: 0.1509 S33: -0.0427 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESID 151:260 REMARK 3 ORIGIN FOR THE GROUP (A): -1.9709 7.7291 18.5355 REMARK 3 T TENSOR REMARK 3 T11: 0.0908 T22: 0.1556 REMARK 3 T33: 0.1875 T12: -0.0142 REMARK 3 T13: 0.0060 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 3.4376 L22: 2.7943 REMARK 3 L33: 1.8536 L12: 0.6459 REMARK 3 L13: 0.2811 L23: 0.4233 REMARK 3 S TENSOR REMARK 3 S11: 0.0464 S12: -0.0363 S13: -0.2082 REMARK 3 S21: -0.0418 S22: -0.0714 S23: 0.1012 REMARK 3 S31: 0.0615 S32: -0.2065 S33: 0.0066 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESID 261:335 REMARK 3 ORIGIN FOR THE GROUP (A): 4.0377 7.2896 -5.0830 REMARK 3 T TENSOR REMARK 3 T11: 0.5497 T22: 0.4999 REMARK 3 T33: 0.3043 T12: -0.2095 REMARK 3 T13: 0.0597 T23: -0.1532 REMARK 3 L TENSOR REMARK 3 L11: 0.9515 L22: 0.2206 REMARK 3 L33: 2.1708 L12: -0.1972 REMARK 3 L13: -0.6291 L23: -0.1419 REMARK 3 S TENSOR REMARK 3 S11: -0.3699 S12: 0.6217 S13: -0.4345 REMARK 3 S21: -0.8393 S22: 0.4124 S23: -0.2447 REMARK 3 S31: 0.1940 S32: -0.0483 S33: 0.0362 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): 18.5025 33.2140 18.5176 REMARK 3 T TENSOR REMARK 3 T11: 0.3116 T22: 0.1822 REMARK 3 T33: 0.3624 T12: -0.0519 REMARK 3 T13: -0.0366 T23: -0.0545 REMARK 3 L TENSOR REMARK 3 L11: 3.0069 L22: 5.7691 REMARK 3 L33: 3.9988 L12: 0.4104 REMARK 3 L13: -0.3109 L23: -0.7547 REMARK 3 S TENSOR REMARK 3 S11: 0.0548 S12: -0.0909 S13: 0.4864 REMARK 3 S21: -0.1555 S22: -0.4681 S23: -0.6902 REMARK 3 S31: 0.0368 S32: -0.1357 S33: 0.2926 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 9Y1G 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_1000299657. 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 : 7.4 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 : 113401 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 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) : 0.68500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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 (%): 49.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 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 7.4, 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 39.92050 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: 4030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 THR A 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 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 GLU A 9 CG CD OE1 OE2 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 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 HOH P 123 O HOH P 150 1.96 REMARK 500 O HOH P 127 O HOH P 129 1.98 REMARK 500 O HOH T 141 O HOH T 158 2.00 REMARK 500 O HOH A 729 O HOH A 776 2.06 REMARK 500 OP2 DG D 5 O HOH D 101 2.08 REMARK 500 O HOH T 104 O HOH T 169 2.09 REMARK 500 O HOH A 726 O HOH P 116 2.09 REMARK 500 OE1 GLN A 213 O HOH A 501 2.10 REMARK 500 O HOH A 800 O HOH P 113 2.10 REMARK 500 O HOH T 114 O HOH P 101 2.12 REMARK 500 O HOH P 108 O HOH P 129 2.13 REMARK 500 O HOH A 640 O HOH A 804 2.14 REMARK 500 O HOH T 115 O HOH T 131 2.15 REMARK 500 O HOH A 841 O HOH T 169 2.16 REMARK 500 O HOH A 530 O HOH A 853 2.16 REMARK 500 O HOH A 700 O HOH A 830 2.16 REMARK 500 O HOH T 148 O HOH T 154 2.17 REMARK 500 O HOH A 807 O HOH A 848 2.17 REMARK 500 O HOH T 164 O HOH T 172 2.18 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 807 O HOH A 825 1455 2.02 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 -0.120 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 7 O4' - C1' - N9 ANGL. DEV. = 3.2 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 43.56 -87.98 REMARK 500 CYS A 178 -157.51 -99.33 REMARK 500 ASN A 245 -114.51 43.77 REMARK 500 ASN A 294 -166.27 -127.74 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 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 90.6 REMARK 620 3 VAL A 65 O 92.4 96.3 REMARK 620 4 HOH A 786 O 87.4 91.1 172.6 REMARK 620 5 DC D 3 OP1 174.7 94.5 88.5 91.1 REMARK 620 6 HOH D 111 O 93.4 173.9 88.2 84.4 81.4 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 THR A 101 O REMARK 620 2 VAL A 103 O 92.7 REMARK 620 3 ILE A 106 O 95.3 85.9 REMARK 620 4 HOH A 764 O 83.6 94.0 178.9 REMARK 620 5 DG P 9 OP1 169.3 94.5 93.1 88.1 REMARK 620 6 HOH P 115 O 83.9 174.0 89.4 90.6 89.5 REMARK 620 N 1 2 3 4 5 DBREF 9Y1G A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 9Y1G T 1 16 PDB 9Y1G 9Y1G 1 16 DBREF 9Y1G P 1 10 PDB 9Y1G 9Y1G 1 10 DBREF 9Y1G D 1 5 PDB 9Y1G 9Y1G 1 5 SEQADV 9Y1G 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 DC 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 CL A 403 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 5 NA 2(NA 1+) FORMUL 7 CL CL 1- FORMUL 8 HOH *567(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 ASN A 128 1 8 HELIX 9 AA9 GLU A 129 LEU A 132 5 4 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 GLY A 237 O ILE A 255 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N SER A 229 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 LYS A 60 NA NA A 402 1555 1555 2.39 LINK O LEU A 62 NA NA A 402 1555 1555 2.44 LINK O VAL A 65 NA NA A 402 1555 1555 2.40 LINK O THR A 101 NA NA A 401 1555 1555 2.28 LINK O VAL A 103 NA NA A 401 1555 1555 2.55 LINK O ILE A 106 NA NA A 401 1555 1555 2.32 LINK NA NA A 401 O HOH A 764 1555 1555 2.43 LINK NA NA A 401 OP1 DG P 9 1555 1555 2.38 LINK NA NA A 401 O HOH P 115 1555 1555 2.58 LINK NA NA A 402 O HOH A 786 1555 1555 2.46 LINK NA NA A 402 OP1 DC D 3 1555 1555 2.83 LINK NA NA A 402 O HOH D 111 1555 1555 2.47 CISPEP 1 GLY A 274 SER A 275 0 2.81 CRYST1 54.374 79.841 55.115 90.00 105.31 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 0.018391 0.000000 0.005035 0.00000 SCALE2 0.000000 0.012525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018811 0.00000 CONECT 433 3296 CONECT 451 3296 CONECT 470 3296 CONECT 765 3295 CONECT 783 3295 CONECT 800 3295 CONECT 3147 3295 CONECT 3232 3296 CONECT 3295 765 783 800 3147 CONECT 3295 3561 3796 CONECT 3296 433 451 470 3232 CONECT 3296 3583 3847 CONECT 3561 3295 CONECT 3583 3296 CONECT 3796 3295 CONECT 3847 3296 MASTER 485 0 3 19 9 0 0 6 3801 4 16 30 END