PDB Short entry for 5U8H HEADER TRANSFERASE,LYASE/DNA 14-DEC-16 5U8H TITLE DNA POLYMERASE BETA G231D CRYSTALLIZED IN PEG 400 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7,4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 9 3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA TEMPLATE STRAND; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: DNA PRIMER STRAND; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: DNA (5'-D(*GP*TP*CP*GP*G)-3'); COMPND 20 CHAIN: D; COMPND 21 ENGINEERED: YES; COMPND 22 OTHER_DETAILS: DNA DOWNSTREAM STRAND 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 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: DNA PRIMER STRAND, 10MER; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 OTHER_DETAILS: DNA DOWNSTREAM STRAND, 5MER; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 24 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, LYASE, DNA COMPLEX, TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.E.ECKENROTH,S.DOUBLIE REVDAT 6 04-OCT-23 5U8H 1 LINK REVDAT 5 04-DEC-19 5U8H 1 REMARK REVDAT 4 16-JAN-19 5U8H 1 SOURCE REVDAT 3 20-SEP-17 5U8H 1 REMARK REVDAT 2 17-MAY-17 5U8H 1 JRNL REVDAT 1 26-APR-17 5U8H 0 JRNL AUTH B.E.ECKENROTH,J.B.TOWLE-WEICKSEL,A.A.NEMEC,D.L.MURPHY, JRNL AUTH 2 J.B.SWEASY,S.DOUBLIE JRNL TITL REMOTE MUTATIONS INDUCE FUNCTIONAL CHANGES IN ACTIVE SITE JRNL TITL 2 RESIDUES OF HUMAN DNA POLYMERASE BETA. JRNL REF BIOCHEMISTRY V. 56 2363 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28402631 JRNL DOI 10.1021/ACS.BIOCHEM.6B01287 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 44548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 4425 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 14.0333 - 6.4767 1.00 1383 187 0.1415 0.1608 REMARK 3 2 6.4767 - 5.2276 1.00 1426 151 0.1537 0.1980 REMARK 3 3 5.2276 - 4.5933 1.00 1419 146 0.1339 0.1751 REMARK 3 4 4.5933 - 4.1855 1.00 1377 140 0.1300 0.1956 REMARK 3 5 4.1855 - 3.8924 1.00 1452 159 0.1391 0.1779 REMARK 3 6 3.8924 - 3.6672 1.00 1375 187 0.1488 0.2060 REMARK 3 7 3.6672 - 3.4865 1.00 1445 155 0.1614 0.2018 REMARK 3 8 3.4865 - 3.3369 1.00 1431 108 0.1735 0.2227 REMARK 3 9 3.3369 - 3.2100 1.00 1373 169 0.1729 0.2600 REMARK 3 10 3.2100 - 3.1005 1.00 1419 188 0.1878 0.2794 REMARK 3 11 3.1005 - 3.0045 1.00 1401 152 0.2002 0.2430 REMARK 3 12 3.0045 - 2.9194 1.00 1397 149 0.2068 0.3011 REMARK 3 13 2.9194 - 2.8432 1.00 1483 125 0.2115 0.2573 REMARK 3 14 2.8432 - 2.7744 1.00 1408 143 0.2197 0.2825 REMARK 3 15 2.7744 - 2.7118 1.00 1363 172 0.2068 0.3072 REMARK 3 16 2.7118 - 2.6544 1.00 1382 177 0.2058 0.2507 REMARK 3 17 2.6544 - 2.6017 1.00 1421 160 0.2082 0.2822 REMARK 3 18 2.6017 - 2.5529 1.00 1462 155 0.2115 0.3038 REMARK 3 19 2.5529 - 2.5076 1.00 1395 172 0.2293 0.2794 REMARK 3 20 2.5076 - 2.4653 0.99 1351 144 0.2169 0.2688 REMARK 3 21 2.4653 - 2.4257 0.99 1459 140 0.2374 0.2990 REMARK 3 22 2.4257 - 2.3886 0.99 1334 144 0.2478 0.2775 REMARK 3 23 2.3886 - 2.3536 0.98 1450 138 0.2437 0.2895 REMARK 3 24 2.3536 - 2.3206 0.96 1352 157 0.2375 0.3002 REMARK 3 25 2.3206 - 2.2894 0.92 1310 119 0.2415 0.2624 REMARK 3 26 2.2894 - 2.2598 0.90 1255 168 0.2525 0.2801 REMARK 3 27 2.2598 - 2.2316 0.79 1134 104 0.2536 0.2830 REMARK 3 28 2.2316 - 2.2049 0.72 1007 112 0.2608 0.2931 REMARK 3 29 2.2049 - 2.1793 0.64 894 104 0.2655 0.3316 REMARK 3 30 2.1793 - 2.1549 0.55 765 100 0.2829 0.2974 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.50 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 : 0.002 3239 REMARK 3 ANGLE : 0.531 4507 REMARK 3 CHIRALITY : 0.023 504 REMARK 3 PLANARITY : 0.002 476 REMARK 3 DIHEDRAL : 17.949 1250 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 9 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.5658 -4.1314 9.3383 REMARK 3 T TENSOR REMARK 3 T11: 0.2072 T22: 0.1511 REMARK 3 T33: 0.1889 T12: -0.0336 REMARK 3 T13: 0.0181 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.8185 L22: 2.6571 REMARK 3 L33: 3.9188 L12: -0.6018 REMARK 3 L13: -0.1440 L23: 0.9512 REMARK 3 S TENSOR REMARK 3 S11: 0.0608 S12: -0.0917 S13: -0.1506 REMARK 3 S21: -0.0624 S22: -0.0283 S23: -0.1539 REMARK 3 S31: 0.2446 S32: -0.1647 S33: -0.0276 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 90 THROUGH 150 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.2516 10.1794 28.9527 REMARK 3 T TENSOR REMARK 3 T11: 0.1606 T22: 0.2610 REMARK 3 T33: 0.1592 T12: -0.0385 REMARK 3 T13: -0.0033 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 4.7986 L22: 1.9812 REMARK 3 L33: 1.7673 L12: -1.2304 REMARK 3 L13: -0.6585 L23: 0.1382 REMARK 3 S TENSOR REMARK 3 S11: 0.1005 S12: -0.7118 S13: -0.0033 REMARK 3 S21: 0.0653 S22: 0.0156 S23: -0.1752 REMARK 3 S31: -0.1529 S32: 0.2329 S33: -0.1132 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 151 THROUGH 260 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.4932 8.6258 18.0219 REMARK 3 T TENSOR REMARK 3 T11: 0.1188 T22: 0.1917 REMARK 3 T33: 0.2134 T12: -0.0190 REMARK 3 T13: 0.0011 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 4.7037 L22: 2.9599 REMARK 3 L33: 3.5917 L12: 0.1321 REMARK 3 L13: -0.1427 L23: -0.6117 REMARK 3 S TENSOR REMARK 3 S11: 0.0687 S12: 0.0690 S13: -0.0051 REMARK 3 S21: -0.1103 S22: 0.0352 S23: 0.1224 REMARK 3 S31: -0.0508 S32: -0.2478 S33: -0.0996 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 261 THROUGH 335 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9587 8.2887 -5.0339 REMARK 3 T TENSOR REMARK 3 T11: 0.5819 T22: 0.6506 REMARK 3 T33: 0.3493 T12: -0.2080 REMARK 3 T13: 0.0150 T23: -0.1347 REMARK 3 L TENSOR REMARK 3 L11: 0.8876 L22: 1.5287 REMARK 3 L33: 2.8934 L12: 0.4110 REMARK 3 L13: -0.6333 L23: -1.3241 REMARK 3 S TENSOR REMARK 3 S11: -0.5617 S12: 0.6013 S13: -0.3044 REMARK 3 S21: -1.0261 S22: 0.7624 S23: -0.0627 REMARK 3 S31: 0.4022 S32: -0.3537 S33: -0.1610 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.6498 14.0755 -3.1618 REMARK 3 T TENSOR REMARK 3 T11: 0.3743 T22: 0.2734 REMARK 3 T33: 0.2401 T12: 0.0819 REMARK 3 T13: 0.0062 T23: 0.0439 REMARK 3 L TENSOR REMARK 3 L11: 6.6521 L22: 3.4212 REMARK 3 L33: 6.9105 L12: 0.6223 REMARK 3 L13: -1.6866 L23: 1.5204 REMARK 3 S TENSOR REMARK 3 S11: -0.0442 S12: 0.0246 S13: 0.7582 REMARK 3 S21: -0.0171 S22: 0.3454 S23: 0.0601 REMARK 3 S31: -0.1487 S32: 0.6390 S33: -0.2485 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 6 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.0306 24.4070 15.0410 REMARK 3 T TENSOR REMARK 3 T11: 0.3186 T22: 0.1703 REMARK 3 T33: 0.3467 T12: -0.0404 REMARK 3 T13: -0.0058 T23: 0.0236 REMARK 3 L TENSOR REMARK 3 L11: 1.6607 L22: 2.4366 REMARK 3 L33: 1.3853 L12: -0.2556 REMARK 3 L13: -0.4300 L23: -0.0738 REMARK 3 S TENSOR REMARK 3 S11: 0.1001 S12: 0.0280 S13: 0.3375 REMARK 3 S21: 0.2852 S22: -0.2016 S23: -0.3705 REMARK 3 S31: 0.0950 S32: -0.0536 S33: 0.0353 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5566 25.7113 15.9914 REMARK 3 T TENSOR REMARK 3 T11: 0.2783 T22: 0.2342 REMARK 3 T33: 0.2572 T12: -0.0065 REMARK 3 T13: -0.0245 T23: -0.0375 REMARK 3 L TENSOR REMARK 3 L11: 1.8324 L22: 5.0243 REMARK 3 L33: 2.9665 L12: 0.2342 REMARK 3 L13: -0.1134 L23: 0.1727 REMARK 3 S TENSOR REMARK 3 S11: 0.2058 S12: 0.0099 S13: 0.1427 REMARK 3 S21: -0.7537 S22: -0.4654 S23: -0.1484 REMARK 3 S31: -0.1181 S32: -0.2061 S33: 0.2924 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.1685 6.3606 -4.2731 REMARK 3 T TENSOR REMARK 3 T11: 0.3392 T22: 0.2790 REMARK 3 T33: 0.2239 T12: 0.0342 REMARK 3 T13: -0.0110 T23: 0.0428 REMARK 3 L TENSOR REMARK 3 L11: 2.9531 L22: 3.1171 REMARK 3 L33: 3.2447 L12: 0.6863 REMARK 3 L13: -0.0273 L23: -0.6779 REMARK 3 S TENSOR REMARK 3 S11: -0.0076 S12: 0.7972 S13: 0.2480 REMARK 3 S21: -0.3402 S22: 0.0187 S23: 0.2533 REMARK 3 S31: 0.0839 S32: 0.2556 S33: -0.0119 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 5U8H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225461. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 104 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23423 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 14.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: 3ISB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 400, 100 MM POTASSIUM SODIUM REMARK 280 TARTRATE, 1% ISOPROPANOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 39.38600 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: 3970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 203 REMARK 465 SER A 204 REMARK 465 THR A 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 PRO A 208 REMARK 465 LYS A 244 REMARK 465 ASN A 245 REMARK 465 ASP A 246 REMARK 465 GLU A 247 REMARK 465 LYS A 248 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 48 CG CD CE NZ REMARK 470 GLN A 90 CG CD OE1 NE2 REMARK 470 LYS A 167 CE NZ REMARK 470 GLU A 186 CG CD OE1 OE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 GLU A 216 CD OE1 OE2 REMARK 470 LYS A 220 CE NZ REMARK 470 GLU A 232 CG CD OE1 OE2 REMARK 470 GLU A 249 CG CD OE1 OE2 REMARK 470 ASP A 276 CG OD1 OD2 REMARK 470 ILE A 277 CG1 CG2 CD1 REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 GLN A 324 CG CD OE1 NE2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 LYS A 331 CG CD CE NZ REMARK 470 GLU A 335 CG CD OE1 OE2 REMARK 470 DC T 1 O5' 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 34.00 -82.02 REMARK 500 CYS A 178 -146.07 -101.73 REMARK 500 ASP A 231 -146.50 -146.69 REMARK 500 ASN A 294 -159.68 -120.64 REMARK 500 ASP A 332 40.05 -108.02 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 T 142 DISTANCE = 6.53 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 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 86.1 REMARK 620 3 VAL A 65 O 86.2 87.5 REMARK 620 4 HOH A 621 O 87.2 82.4 168.3 REMARK 620 5 DC D 3 OP1 175.1 97.6 90.6 96.5 REMARK 620 6 HOH D 101 O 95.8 169.2 82.0 108.3 80.0 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 92.7 REMARK 620 3 ILE A 106 O 88.0 83.2 REMARK 620 4 HOH A 637 O 82.3 90.1 167.9 REMARK 620 5 DG P 9 OP1 168.3 97.3 99.1 91.7 REMARK 620 6 HOH P 118 O 77.9 169.3 91.2 93.8 92.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5U8I RELATED DB: PDB REMARK 900 RELATED ID: 5U8G RELATED DB: PDB DBREF 5U8H A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 5U8H T 1 16 PDB 5U8H 5U8H 1 16 DBREF 5U8H P 1 10 PDB 5U8H 5U8H 1 10 DBREF 5U8H D 1 5 PDB 5U8H 5U8H 1 5 SEQADV 5U8H ASP A 231 UNP P06746 GLY 231 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 SER 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 ASP 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 DA 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 HETNAM NA SODIUM ION FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *249(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 GLY A 179 ARG A 182 5 4 HELIX 14 AB5 LEU A 210 VAL A 221 1 12 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 GLY A 290 1 16 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 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 401 1555 1555 2.54 LINK O LEU A 62 NA NA A 401 1555 1555 2.59 LINK O VAL A 65 NA NA A 401 1555 1555 2.51 LINK O THR A 101 NA NA A 402 1555 1555 2.33 LINK O VAL A 103 NA NA A 402 1555 1555 2.51 LINK O ILE A 106 NA NA A 402 1555 1555 2.54 LINK NA NA A 401 O HOH A 621 1555 1555 2.70 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.62 LINK NA NA A 401 O HOH D 101 1555 1555 2.48 LINK NA NA A 402 O HOH A 637 1555 1555 2.50 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.33 LINK NA NA A 402 O HOH P 118 1555 1555 2.51 CISPEP 1 GLY A 274 SER A 275 0 2.48 SITE 1 AC1 6 LYS A 60 LEU A 62 VAL A 65 HOH A 621 SITE 2 AC1 6 DC D 3 HOH D 101 SITE 1 AC2 6 THR A 101 VAL A 103 ILE A 106 HOH A 637 SITE 2 AC2 6 DG P 9 HOH P 118 CRYST1 54.085 78.772 54.686 90.00 104.45 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 0.018489 0.000000 0.004766 0.00000 SCALE2 0.000000 0.012695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018884 0.00000