HEADER TRANSFERASE/DNA 29-AUG-23 8U0P TITLE SYNAPTIC COMPLEX OF HUMAN DNA POLYMERASE LAMBDA DL VARIANT ENGAGED ON TITLE 2 A NONCOMPLEMENTARY DNA DOUBLE-STRAND BREAK 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 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-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_PLASMID: PGEXM; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 21 ORGANISM_TAXID: 32630 KEYWDS NONHOMOLOGOUS END-JOINING, BASE EXCISION REPAIR, DNA POLYMERASE, KEYWDS 2 TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.M.KAMINSKI,L.C.PEDERSEN,K.BEBENEK,T.A.KUNKEL,K.K.CHIRUVELLA, AUTHOR 2 D.A.RAMSDEN REVDAT 1 13-MAR-24 8U0P 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 DNA POLYMERASE LAMBDA LOOP1 VARIANT YIELDS UNEXPECTED JRNL TITL 2 GAIN-OF-FUNCTION CAPABILITIES IN NONHOMOLOGOUS END-JOINING. JRNL REF DNA REPAIR (AMST) V. 136 03645 2024 JRNL REFN ISSN 1568-7856 JRNL PMID 38428373 JRNL DOI 10.1016/J.DNAREP.2024.103645 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 38638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1935 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 39.4000 - 4.5300 0.97 2796 147 0.1638 0.1738 REMARK 3 2 4.5300 - 3.5900 1.00 2751 144 0.1395 0.1401 REMARK 3 3 3.5900 - 3.1400 1.00 2694 148 0.1618 0.1828 REMARK 3 4 3.1400 - 2.8500 0.99 2691 137 0.1804 0.1997 REMARK 3 5 2.8500 - 2.6500 0.99 2656 134 0.1851 0.2204 REMARK 3 6 2.6500 - 2.4900 1.00 2683 139 0.1836 0.1967 REMARK 3 7 2.4900 - 2.3700 0.99 2650 136 0.1809 0.2218 REMARK 3 8 2.3700 - 2.2600 0.99 2657 145 0.1731 0.2183 REMARK 3 9 2.2600 - 2.1800 0.99 2616 143 0.1921 0.2408 REMARK 3 10 2.1800 - 2.1000 0.99 2622 130 0.1861 0.2152 REMARK 3 11 2.1000 - 2.0400 0.99 2629 149 0.1839 0.2335 REMARK 3 12 2.0400 - 1.9800 0.97 2565 134 0.2004 0.2270 REMARK 3 13 1.9800 - 1.9300 0.98 2583 141 0.2280 0.2550 REMARK 3 14 1.9300 - 1.9000 0.80 2110 108 0.2773 0.3184 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) : 0.198 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.488 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.17 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 : 0.005 3111 REMARK 3 ANGLE : 0.719 4324 REMARK 3 CHIRALITY : 0.045 482 REMARK 3 PLANARITY : 0.007 472 REMARK 3 DIHEDRAL : 11.534 930 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 237:329 REMARK 3 ORIGIN FOR THE GROUP (A): -7.5220 25.5375 -26.5772 REMARK 3 T TENSOR REMARK 3 T11: 0.4985 T22: 0.4368 REMARK 3 T33: 0.4001 T12: -0.1047 REMARK 3 T13: 0.1448 T23: -0.0459 REMARK 3 L TENSOR REMARK 3 L11: 0.7527 L22: 1.5712 REMARK 3 L33: 1.2690 L12: -0.1172 REMARK 3 L13: 0.2513 L23: 0.0039 REMARK 3 S TENSOR REMARK 3 S11: 0.0381 S12: 0.3478 S13: -0.0107 REMARK 3 S21: -0.6893 S22: 0.2461 S23: -0.5815 REMARK 3 S31: -0.3987 S32: 0.3251 S33: -0.2425 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 330:386 REMARK 3 ORIGIN FOR THE GROUP (A): -13.8917 20.1798 0.7762 REMARK 3 T TENSOR REMARK 3 T11: 0.1616 T22: 0.1909 REMARK 3 T33: 0.1780 T12: 0.0115 REMARK 3 T13: -0.0129 T23: -0.0419 REMARK 3 L TENSOR REMARK 3 L11: 1.2572 L22: 2.1798 REMARK 3 L33: 1.1836 L12: -0.1616 REMARK 3 L13: 0.2968 L23: -0.2374 REMARK 3 S TENSOR REMARK 3 S11: -0.0996 S12: -0.2267 S13: 0.1510 REMARK 3 S21: 0.1227 S22: 0.1367 S23: -0.1095 REMARK 3 S31: -0.0729 S32: -0.1723 S33: -0.0420 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 387:495 REMARK 3 ORIGIN FOR THE GROUP (A): -11.3316 -5.1167 -7.7709 REMARK 3 T TENSOR REMARK 3 T11: 0.2059 T22: 0.1595 REMARK 3 T33: 0.2589 T12: -0.0267 REMARK 3 T13: -0.0239 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 1.2535 L22: 1.0950 REMARK 3 L33: 2.4138 L12: -0.4363 REMARK 3 L13: 0.4621 L23: 0.3991 REMARK 3 S TENSOR REMARK 3 S11: 0.1249 S12: -0.0008 S13: -0.3374 REMARK 3 S21: 0.0875 S22: 0.0260 S23: -0.0052 REMARK 3 S31: 0.3489 S32: -0.0470 S33: -0.1486 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 496:575 REMARK 3 ORIGIN FOR THE GROUP (A): -19.2314 1.7651 -27.8588 REMARK 3 T TENSOR REMARK 3 T11: 0.2461 T22: 0.2383 REMARK 3 T33: 0.1786 T12: 0.0020 REMARK 3 T13: -0.0069 T23: -0.0476 REMARK 3 L TENSOR REMARK 3 L11: 1.2339 L22: 2.1067 REMARK 3 L33: 1.8724 L12: 0.2036 REMARK 3 L13: 0.6914 L23: 0.2801 REMARK 3 S TENSOR REMARK 3 S11: 0.0225 S12: 0.2694 S13: -0.0862 REMARK 3 S21: -0.3764 S22: 0.0223 S23: 0.0263 REMARK 3 S31: 0.0352 S32: 0.0370 S33: -0.0451 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -25.3383 15.0589 -16.6921 REMARK 3 T TENSOR REMARK 3 T11: 0.1631 T22: 0.2092 REMARK 3 T33: 0.1460 T12: 0.0097 REMARK 3 T13: -0.0158 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 1.2457 L22: 0.9965 REMARK 3 L33: 1.5225 L12: 0.3086 REMARK 3 L13: -0.5398 L23: 0.8995 REMARK 3 S TENSOR REMARK 3 S11: -0.0064 S12: 0.2150 S13: 0.0585 REMARK 3 S21: -0.1387 S22: -0.0103 S23: 0.1894 REMARK 3 S31: -0.0986 S32: -0.1824 S33: 0.0363 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 8U0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000276476. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-21 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 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 : 38985 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 19.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.73000 REMARK 200 FOR SHELL : 1.580 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85 MM NA CACODYLATE PH 6.5, 0.17 M REMARK 280 AMMONIUM SULFATE, 25.5 % (W/V) PEG 8000, 15% (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 28.10250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.36450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.03400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.36450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.10250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.03400 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: 5700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 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 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 465 PRO A 547 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 ASP A 237 OD1 OD2 REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 THR A 250 OG1 CG2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 258 CD OE1 OE2 REMARK 470 LYS A 259 CE NZ 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 LEU A 317 CD1 CD2 REMARK 470 GLU A 318 OE1 OE2 REMARK 470 ARG A 323 CD NE CZ NH1 NH2 REMARK 470 LYS A 324 CE NZ REMARK 470 GLU A 330 CD OE1 OE2 REMARK 470 GLU A 385 CD OE1 OE2 REMARK 470 GLU A 390 CD OE1 OE2 REMARK 470 ARG A 438 CD NE CZ NH1 NH2 REMARK 470 ARG A 441 NE CZ NH1 NH2 REMARK 470 ARG A 446 CZ NH1 NH2 REMARK 470 GLN A 453 CD OE1 NE2 REMARK 470 GLU A 454 CD OE1 OE2 REMARK 470 GLN A 464 CD OE1 NE2 REMARK 470 LYS A 523 NZ REMARK 470 LYS A 557 CE NZ 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 OP2 DG T 2 O HOH T 101 2.12 REMARK 500 O HOH P 103 O HOH P 126 2.16 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 -0.127 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 THR A 250 63.19 -114.31 REMARK 500 CYS A 415 -137.32 -110.14 REMARK 500 ARG A 438 -29.23 -141.22 REMARK 500 ASP A 459 144.11 -174.38 REMARK 500 SER A 463 25.93 -143.90 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 130 DISTANCE = 6.12 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 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 103.1 REMARK 620 3 ALA A 344 O 88.0 88.4 REMARK 620 4 HOH A 901 O 84.8 96.6 172.0 REMARK 620 5 DA P 5 OP1 158.1 98.8 92.7 92.6 REMARK 620 6 HOH P 102 O 71.3 169.8 82.9 91.5 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 92.1 REMARK 620 3 DUP A 609 O2A 96.8 87.4 REMARK 620 4 DUP A 609 O2B 170.4 92.6 91.9 REMARK 620 5 DUP A 609 O3G 88.0 179.6 93.0 87.3 REMARK 620 6 HOH A 777 O 83.2 88.8 176.2 88.5 90.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD1 88.3 REMARK 620 3 ASP A 490 OD2 93.0 98.6 REMARK 620 4 DUP A 609 O2A 94.5 85.5 171.5 REMARK 620 5 HOH A 779 O 88.0 164.4 96.7 79.7 REMARK 620 6 DC P 6 O3' 164.4 90.8 71.7 100.9 96.8 REMARK 620 N 1 2 3 4 5 DBREF 8U0P A 234 464 UNP Q9UGP5 DPOLL_HUMAN 234 464 DBREF 8U0P A 472 575 UNP Q9UGP5 DPOLL_HUMAN 472 575 DBREF 8U0P T 1 11 PDB 8U0P 8U0P 1 11 DBREF 8U0P P 1 6 PDB 8U0P 8U0P 1 6 DBREF 8U0P D 1 4 PDB 8U0P 8U0P 1 4 SEQADV 8U0P GLY A 230 UNP Q9UGP5 EXPRESSION TAG SEQADV 8U0P SER A 231 UNP Q9UGP5 EXPRESSION TAG SEQADV 8U0P ALA A 232 UNP Q9UGP5 EXPRESSION TAG SEQADV 8U0P ALA A 233 UNP Q9UGP5 EXPRESSION TAG SEQADV 8U0P GLY A 471 UNP Q9UGP5 LINKER SEQRES 1 A 340 GLY SER ALA ALA ALA VAL LEU ASP LYS TRP VAL CYS ALA SEQRES 2 A 340 GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU HIS SEQRES 3 A 340 ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SER SEQRES 4 A 340 VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA LYS SEQRES 5 A 340 ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL THR SEQRES 6 A 340 SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY LYS SEQRES 7 A 340 ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER GLY SEQRES 8 A 340 HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL PRO SEQRES 9 A 340 VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY THR SEQRES 10 A 340 LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SER SEQRES 11 A 340 LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR GLN SEQRES 12 A 340 GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU GLU SEQRES 13 A 340 ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN THR SEQRES 14 A 340 VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU LEU SEQRES 15 A 340 CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA THR SEQRES 16 A 340 CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP GLY SEQRES 17 A 340 ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SER SEQRES 18 A 340 LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SER SEQRES 19 A 340 GLN GLY LYS TYR LEU GLY VAL CYS ARG LEU PRO GLY PRO SEQRES 20 A 340 GLY ARG ARG HIS ARG ARG LEU ASP ILE ILE VAL VAL PRO SEQRES 21 A 340 TYR SER GLU PHE ALA CYS ALA LEU LEU TYR PHE THR GLY SEQRES 22 A 340 SER ALA HIS PHE ASN ARG SER MET ARG ALA LEU ALA LYS SEQRES 23 A 340 THR LYS GLY MET SER LEU SER GLU HIS ALA LEU SER THR SEQRES 24 A 340 ALA VAL VAL ARG ASN THR HIS GLY CYS LYS VAL GLY PRO SEQRES 25 A 340 GLY ARG VAL LEU PRO THR PRO THR GLU LYS ASP VAL PHE SEQRES 26 A 340 ARG LEU LEU GLY LEU PRO TYR ARG GLU PRO ALA GLU ARG SEQRES 27 A 340 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 MG A 601 1 HET NA A 602 1 HET MG A 603 1 HET CL A 604 1 HET CL A 605 1 HET CL A 606 1 HET CL A 607 1 HET SO4 A 608 5 HET DUP A 609 28 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE FORMUL 5 MG 2(MG 2+) FORMUL 6 NA NA 1+ FORMUL 8 CL 4(CL 1-) FORMUL 12 SO4 O4 S 2- FORMUL 13 DUP C9 H16 N3 O13 P3 FORMUL 14 HOH *347(H2 O) HELIX 1 AA1 TRP A 239 GLN A 243 5 5 HELIX 2 AA2 PRO A 244 ASN A 251 5 8 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 TYR A 473 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 SER A 339 NA NA A 602 1555 1555 2.36 LINK O ILE A 341 NA NA A 602 1555 1555 2.32 LINK O ALA A 344 NA NA A 602 1555 1555 2.29 LINK OD1 ASP A 427 MG MG A 601 1555 1555 1.96 LINK OD2 ASP A 427 MG MG A 603 1555 1555 1.98 LINK OD2 ASP A 429 MG MG A 601 1555 1555 2.09 LINK OD1 ASP A 429 MG MG A 603 1555 1555 2.18 LINK OD2 ASP A 490 MG MG A 603 1555 1555 2.09 LINK MG MG A 601 O2A DUP A 609 1555 1555 2.08 LINK MG MG A 601 O2B DUP A 609 1555 1555 2.05 LINK MG MG A 601 O3G DUP A 609 1555 1555 2.07 LINK MG MG A 601 O HOH A 777 1555 1555 2.15 LINK NA NA A 602 O HOH A 901 1555 1555 2.43 LINK NA NA A 602 OP1 DA P 5 1555 1555 2.35 LINK NA NA A 602 O HOH P 102 1555 1555 2.88 LINK MG MG A 603 O2A DUP A 609 1555 1555 2.40 LINK MG MG A 603 O HOH A 779 1555 1555 2.25 LINK MG MG A 603 O3' DC P 6 1555 1555 2.51 CISPEP 1 GLY A 508 SER A 509 0 2.46 CRYST1 56.205 60.068 140.729 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 0.016648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007106 0.00000 CONECT 753 2969 CONECT 767 2969 CONECT 793 2969 CONECT 1463 2968 CONECT 1464 2970 CONECT 1478 2970 CONECT 1479 2968 CONECT 1908 2970 CONECT 2844 2969 CONECT 2872 2970 CONECT 2968 1463 1479 2998 3002 CONECT 2968 3007 3085 CONECT 2969 753 767 793 2844 CONECT 2969 3211 3318 CONECT 2970 1464 1478 1908 2872 CONECT 2970 2998 3087 CONECT 2975 2976 2977 2978 2979 CONECT 2976 2975 CONECT 2977 2975 CONECT 2978 2975 CONECT 2979 2975 CONECT 2980 2981 CONECT 2981 2980 2982 2984 CONECT 2982 2981 2983 CONECT 2983 2982 2987 CONECT 2984 2981 2985 CONECT 2985 2984 2986 2987 CONECT 2986 2985 CONECT 2987 2983 2985 2988 CONECT 2988 2987 2989 2992 CONECT 2989 2988 2990 CONECT 2990 2989 2991 2993 CONECT 2991 2990 CONECT 2992 2988 2993 CONECT 2993 2990 2992 2994 CONECT 2994 2993 2995 CONECT 2995 2994 2996 CONECT 2996 2995 2997 2998 2999 CONECT 2997 2996 CONECT 2998 2968 2970 2996 CONECT 2999 2996 3000 CONECT 3000 2999 3001 3002 3003 CONECT 3001 3000 CONECT 3002 2968 3000 CONECT 3003 3000 3004 CONECT 3004 3003 3005 3006 3007 CONECT 3005 3004 CONECT 3006 3004 CONECT 3007 2968 3004 CONECT 3085 2968 CONECT 3087 2970 CONECT 3211 2969 CONECT 3318 2969 MASTER 441 0 9 20 9 0 0 6 3264 4 53 30 END