PDB Short entry for 4PPX HEADER TRANSFERASE, LYASE/DNA 27-FEB-14 4PPX TITLE DNA POLYMERASE BETA E295K WITH SPIROIMINODIHYDANTOIN IN TEMPLATING TITLE 2 POSITION 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: 5'-D(*CP*CP*GP*AP*CP*(SDH)P*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: 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: 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(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 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 MOL_ID: 4; SOURCE 16 SYNTHETIC: YES KEYWDS DNA POLYMERASE, DNA COMPLEX, TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.E.ECKENROTH,S.DOUBLIE REVDAT 4 20-SEP-23 4PPX 1 REMARK SEQADV LINK REVDAT 3 22-NOV-17 4PPX 1 REMARK REVDAT 2 23-APR-14 4PPX 1 JRNL REVDAT 1 02-APR-14 4PPX 0 JRNL AUTH B.E.ECKENROTH,A.M.FLEMING,J.B.SWEASY,C.J.BURROWS,S.DOUBLIE JRNL TITL CRYSTAL STRUCTURE OF DNA POLYMERASE BETA WITH DNA CONTAINING JRNL TITL 2 THE BASE LESION SPIROIMINODIHYDANTOIN IN A TEMPLATING JRNL TITL 3 POSITION. JRNL REF BIOCHEMISTRY V. 53 2075 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24649945 JRNL DOI 10.1021/BI500270E REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 25836 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) : 0.177 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2606 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 13.6845 - 6.2575 0.98 1544 207 0.1626 0.1698 REMARK 3 2 6.2575 - 5.0484 0.98 1527 164 0.1601 0.1921 REMARK 3 3 5.0484 - 4.4350 0.98 1573 158 0.1400 0.1738 REMARK 3 4 4.4350 - 4.0410 0.97 1557 182 0.1387 0.1673 REMARK 3 5 4.0410 - 3.7578 0.98 1503 182 0.1474 0.1718 REMARK 3 6 3.7578 - 3.5403 0.96 1510 175 0.1541 0.1842 REMARK 3 7 3.5403 - 3.3657 0.97 1568 128 0.1700 0.2108 REMARK 3 8 3.3657 - 3.2212 0.97 1504 179 0.1738 0.2207 REMARK 3 9 3.2212 - 3.0987 0.96 1485 188 0.1813 0.2312 REMARK 3 10 3.0987 - 2.9929 0.96 1501 169 0.1980 0.2611 REMARK 3 11 2.9929 - 2.9003 0.96 1561 139 0.2009 0.2870 REMARK 3 12 2.9003 - 2.8181 0.95 1545 133 0.1941 0.2061 REMARK 3 13 2.8181 - 2.7445 0.95 1443 182 0.1940 0.2533 REMARK 3 14 2.7445 - 2.6781 0.95 1499 194 0.1867 0.2232 REMARK 3 15 2.6781 - 2.6176 0.94 1477 159 0.1845 0.2627 REMARK 3 16 2.6176 - 2.5623 0.95 1504 170 0.1897 0.2566 REMARK 3 17 2.5623 - 2.5113 0.94 1487 170 0.1915 0.2569 REMARK 3 18 2.5113 - 2.4642 0.94 1463 161 0.1946 0.2636 REMARK 3 19 2.4642 - 2.4205 0.93 1550 144 0.2015 0.2399 REMARK 3 20 2.4205 - 2.3796 0.94 1454 150 0.2075 0.2995 REMARK 3 21 2.3796 - 2.3414 0.94 1448 154 0.2159 0.2534 REMARK 3 22 2.3414 - 2.3056 0.92 1494 170 0.2095 0.2491 REMARK 3 23 2.3056 - 2.2718 0.91 1413 163 0.2042 0.2618 REMARK 3 24 2.2718 - 2.2400 0.91 1426 161 0.2152 0.3136 REMARK 3 25 2.2400 - 2.2098 0.88 1395 152 0.2196 0.2411 REMARK 3 26 2.2098 - 2.1813 0.85 1317 138 0.2219 0.2726 REMARK 3 27 2.1813 - 2.1541 0.79 1266 155 0.2143 0.2421 REMARK 3 28 2.1541 - 2.1282 0.73 1132 132 0.2308 0.3029 REMARK 3 29 2.1282 - 2.1036 0.64 981 122 0.2507 0.2676 REMARK 3 30 2.1036 - 2.0800 0.55 848 114 0.2515 0.2750 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.20 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 3227 REMARK 3 ANGLE : 0.666 4490 REMARK 3 CHIRALITY : 0.040 494 REMARK 3 PLANARITY : 0.002 474 REMARK 3 DIHEDRAL : 20.041 1275 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 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.6008 -3.8434 9.9116 REMARK 3 T TENSOR REMARK 3 T11: 0.2031 T22: 0.1454 REMARK 3 T33: 0.2134 T12: -0.0068 REMARK 3 T13: 0.0198 T23: 0.0345 REMARK 3 L TENSOR REMARK 3 L11: 2.7547 L22: 3.4282 REMARK 3 L33: 2.6758 L12: 0.5538 REMARK 3 L13: 0.1416 L23: 0.9749 REMARK 3 S TENSOR REMARK 3 S11: -0.0173 S12: -0.1429 S13: -0.4040 REMARK 3 S21: -0.1442 S22: 0.0574 S23: -0.3474 REMARK 3 S31: 0.2785 S32: -0.0363 S33: -0.0100 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 91 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0355 10.1304 29.4090 REMARK 3 T TENSOR REMARK 3 T11: 0.1903 T22: 0.2567 REMARK 3 T33: 0.1716 T12: -0.0048 REMARK 3 T13: -0.0076 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 4.3444 L22: 2.0169 REMARK 3 L33: 1.8724 L12: -0.2093 REMARK 3 L13: -0.2234 L23: -0.0956 REMARK 3 S TENSOR REMARK 3 S11: 0.0210 S12: -0.5948 S13: -0.0912 REMARK 3 S21: 0.1994 S22: -0.0388 S23: -0.1689 REMARK 3 S31: -0.1088 S32: 0.2598 S33: 0.0312 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 150 THROUGH 261 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.9144 8.1984 18.4412 REMARK 3 T TENSOR REMARK 3 T11: 0.1428 T22: 0.2015 REMARK 3 T33: 0.1949 T12: 0.0062 REMARK 3 T13: 0.0064 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 4.8445 L22: 3.1119 REMARK 3 L33: 2.6391 L12: -0.0199 REMARK 3 L13: 0.7727 L23: 0.0569 REMARK 3 S TENSOR REMARK 3 S11: 0.1234 S12: 0.1248 S13: -0.1388 REMARK 3 S21: -0.1362 S22: 0.0238 S23: 0.1514 REMARK 3 S31: 0.0348 S32: -0.2364 S33: -0.1379 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.9067 14.1543 -2.8863 REMARK 3 T TENSOR REMARK 3 T11: 0.3613 T22: 0.3066 REMARK 3 T33: 0.2638 T12: 0.0994 REMARK 3 T13: 0.0169 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 4.2027 L22: 4.1203 REMARK 3 L33: 3.7907 L12: -0.3171 REMARK 3 L13: -0.6013 L23: 0.0608 REMARK 3 S TENSOR REMARK 3 S11: -0.0001 S12: 0.2297 S13: 0.5636 REMARK 3 S21: -0.2026 S22: 0.1390 S23: -0.1926 REMARK 3 S31: 0.4546 S32: 0.6315 S33: -0.1740 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.1398 25.5642 15.9065 REMARK 3 T TENSOR REMARK 3 T11: 0.2931 T22: 0.2096 REMARK 3 T33: 0.3015 T12: -0.0250 REMARK 3 T13: 0.0069 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 1.8708 L22: 3.2558 REMARK 3 L33: 1.7985 L12: -0.1030 REMARK 3 L13: 0.1114 L23: 0.2273 REMARK 3 S TENSOR REMARK 3 S11: 0.1169 S12: -0.0070 S13: 0.4418 REMARK 3 S21: -0.3906 S22: -0.2667 S23: -0.0578 REMARK 3 S31: -0.2718 S32: -0.0639 S33: 0.1808 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.3330 6.4899 -3.9711 REMARK 3 T TENSOR REMARK 3 T11: 0.3961 T22: 0.2063 REMARK 3 T33: 0.2085 T12: -0.0352 REMARK 3 T13: 0.0114 T23: 0.0207 REMARK 3 L TENSOR REMARK 3 L11: 4.1705 L22: 2.3128 REMARK 3 L33: 1.6884 L12: 0.5961 REMARK 3 L13: -0.2177 L23: -0.0945 REMARK 3 S TENSOR REMARK 3 S11: 0.1513 S12: 0.6065 S13: 0.2379 REMARK 3 S21: -0.3795 S22: 0.0368 S23: 0.1588 REMARK 3 S31: 0.3255 S32: 0.1558 S33: -0.2885 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'T' AND (RESID 6 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.7752 24.0057 14.9429 REMARK 3 T TENSOR REMARK 3 T11: 0.2846 T22: 0.1798 REMARK 3 T33: 0.3199 T12: -0.0067 REMARK 3 T13: -0.0179 T23: 0.0319 REMARK 3 L TENSOR REMARK 3 L11: 1.7420 L22: 2.0566 REMARK 3 L33: 0.7276 L12: -0.1860 REMARK 3 L13: -0.1304 L23: -0.4273 REMARK 3 S TENSOR REMARK 3 S11: 0.1020 S12: 0.1034 S13: 0.3568 REMARK 3 S21: 0.1967 S22: -0.1423 S23: -0.3262 REMARK 3 S31: -0.0050 S32: 0.2197 S33: 0.0262 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 262 THROUGH 335 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6346 6.1248 -3.4414 REMARK 3 T TENSOR REMARK 3 T11: 0.5181 T22: 0.7773 REMARK 3 T33: 0.3656 T12: -0.0483 REMARK 3 T13: 0.0124 T23: -0.2155 REMARK 3 L TENSOR REMARK 3 L11: 1.6857 L22: 1.9470 REMARK 3 L33: 2.3442 L12: 0.7530 REMARK 3 L13: -0.5678 L23: -0.8707 REMARK 3 S TENSOR REMARK 3 S11: -0.2299 S12: 0.8185 S13: -0.3728 REMARK 3 S21: -0.8361 S22: 0.4757 S23: -0.2966 REMARK 3 S31: 0.4563 S32: 0.1101 S33: -0.2731 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 4PPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000085075. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25842 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 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 (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.26100 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: NULL REMARK 200 SOFTWARE USED: PHASER 2.5.1 REMARK 200 STARTING MODEL: PDB ENTRY 4M9G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350, 300 MM SODIUM ACETATE, PH REMARK 280 9.0, 50 MM HEPES, 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 39.55100 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: 4020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 THR A 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 PRO A 208 REMARK 465 ASN A 245 REMARK 465 ASP A 246 REMARK 465 GLU A 247 REMARK 465 LYS A 248 REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 GLY A 305 REMARK 465 VAL A 306 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 THR A 10 OG1 CG2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 LYS A 81 CE NZ REMARK 470 LYS A 113 CE NZ REMARK 470 ASP A 130 OD1 OD2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 SER A 204 OG REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 LYS A 220 CD CE NZ REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ILE A 277 CG1 CG2 CD1 REMARK 470 LYS A 280 CG CD CE NZ REMARK 470 ARG A 283 CD NE CZ NH1 NH2 REMARK 470 HIS A 285 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 287 CG CD1 CD2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 LYS A 289 CD CE NZ REMARK 470 ARG A 299 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 301 CG CD1 CD2 REMARK 470 GLN A 324 CG CD OE1 NE2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 LYS A 331 CE NZ REMARK 470 GLU A 335 CG CD OE1 OE2 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 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG T 15 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC P 10 O4' - C1' - N1 ANGL. DEV. = 2.3 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 LEU A 11 -74.11 -64.65 REMARK 500 PRO A 50 33.00 -85.73 REMARK 500 CYS A 178 -140.13 -104.28 REMARK 500 ASN A 294 -161.63 -111.46 REMARK 500 ARG A 333 32.67 -95.91 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 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 89.4 REMARK 620 3 VAL A 65 O 83.8 90.7 REMARK 620 4 HOH A 566 O 91.1 92.9 173.7 REMARK 620 5 DC D 3 OP1 174.9 93.4 91.9 93.0 REMARK 620 6 HOH D 102 O 96.2 174.4 90.0 86.8 81.0 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 92.1 REMARK 620 3 ILE A 106 O 91.9 85.3 REMARK 620 4 HOH A 521 O 81.8 95.6 173.7 REMARK 620 5 DG P 9 OP1 168.9 97.0 95.2 90.9 REMARK 620 6 HOH P 101 O 78.0 169.0 90.3 87.7 93.3 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 DBREF 4PPX A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4PPX T 1 16 PDB 4PPX 4PPX 1 16 DBREF 4PPX P 1 10 PDB 4PPX 4PPX 1 10 DBREF 4PPX D 1 5 PDB 4PPX 4PPX 1 5 SEQADV 4PPX LYS A 295 UNP P06746 GLU 295 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 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 LYS 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 SDH 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 MODRES 4PPX SDH T 6 DG HET SDH T 6 24 HET NA A 401 1 HET NA A 402 1 HETNAM SDH (5S)-7-AMINO-1-[2-DEOXY-5-O-(TRIHYDROXY-LAMBDA~5~- HETNAM 2 SDH PHOSPHANYL)-BETA-D-ERYTHRO-PENTOFURANOSYL]-1,3,6,8- HETNAM 3 SDH TETRAAZASPIRO[4.4]NON-7-ENE-2,4,9-TRIONE HETNAM NA SODIUM ION FORMUL 2 SDH C10 H16 N5 O9 P FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *348(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 LYS A 48 1 17 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 THR A 101 1 11 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 LYS A 127 1 7 HELIX 9 9 ASN A 128 LEU A 132 5 5 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 GLU A 147 1 6 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 CYS A 178 ARG A 183 1 6 HELIX 14 14 LEU A 210 VAL A 221 1 12 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 GLU A 288 1 14 HELIX 18 18 SER A 315 ILE A 323 1 9 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 VAL A 177 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DC T 5 P SDH T 6 1555 1555 1.63 LINK O3' SDH T 6 P DG T 7 1555 1555 1.58 LINK O LYS A 60 NA NA A 401 1555 1555 2.43 LINK O LEU A 62 NA NA A 401 1555 1555 2.51 LINK O VAL A 65 NA NA A 401 1555 1555 2.52 LINK O THR A 101 NA NA A 402 1555 1555 2.30 LINK O VAL A 103 NA NA A 402 1555 1555 2.52 LINK O ILE A 106 NA NA A 402 1555 1555 2.48 LINK NA NA A 401 O HOH A 566 1555 1555 2.64 LINK NA NA A 401 OP1 DC D 3 1555 1555 2.66 LINK NA NA A 401 O HOH D 102 1555 1555 2.47 LINK NA NA A 402 O HOH A 521 1555 1555 2.62 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.32 LINK NA NA A 402 O HOH P 101 1555 1555 2.53 CISPEP 1 GLY A 274 SER A 275 0 1.49 SITE 1 AC1 6 LYS A 60 LEU A 62 VAL A 65 HOH A 566 SITE 2 AC1 6 DC D 3 HOH D 102 SITE 1 AC2 6 THR A 101 VAL A 103 ILE A 106 HOH A 521 SITE 2 AC2 6 DG P 9 HOH P 101 CRYST1 54.276 79.102 54.742 90.00 105.40 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 0.018424 0.000000 0.005074 0.00000 SCALE2 0.000000 0.012642 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018948 0.00000