PDB Short entry for 3RRG HEADER TRANSFERASE/DNA 29-APR-11 3RRG TITLE TERNARY STRUCTURE OF THE LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO TITLE 2 AN ABASIC SITE AND A DDGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW FRAGMENT; COMPND 5 SYNONYM: TAQ POLYMERASE 1; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3'); COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: DNA PRIMER; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: (5'-D(*AP*AP*AP*(3DR)P*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- COMPND 15 3'); COMPND 16 CHAIN: C; COMPND 17 FRAGMENT: DNA TEMPLATE; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POL I, POL1, POLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21-B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS DNA POLYMERASE, ABASIC SITE, TRANSLESION SYNTHESIS, A-RULE, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID REVDAT 4 13-SEP-23 3RRG 1 REMARK LINK REVDAT 3 09-MAY-12 3RRG 1 JRNL REVDAT 2 22-FEB-12 3RRG 1 JRNL REVDAT 1 15-FEB-12 3RRG 0 JRNL AUTH S.OBEID,W.WELTE,K.DIEDERICHS,A.MARX JRNL TITL AMINO ACID TEMPLATING MECHANISMS IN SELECTION OF NUCLEOTIDES JRNL TITL 2 OPPOSITE ABASIC SITES BY A FAMILY A DNA POLYMERASE. JRNL REF J.BIOL.CHEM. V. 287 14099 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22318723 JRNL DOI 10.1074/JBC.M111.334904 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_704) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 54951 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 2813 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 47.7625 - 6.2390 1.00 2595 150 0.1453 0.1886 REMARK 3 2 6.2390 - 4.9537 1.00 2615 151 0.1623 0.2107 REMARK 3 3 4.9537 - 4.3280 1.00 2606 114 0.1409 0.1921 REMARK 3 4 4.3280 - 3.9325 1.00 2608 165 0.1545 0.2147 REMARK 3 5 3.9325 - 3.6507 1.00 2578 165 0.1810 0.2488 REMARK 3 6 3.6507 - 3.4356 1.00 2594 151 0.1871 0.2320 REMARK 3 7 3.4356 - 3.2635 1.00 2607 142 0.2007 0.2606 REMARK 3 8 3.2635 - 3.1215 1.00 2609 148 0.2055 0.2756 REMARK 3 9 3.1215 - 3.0014 1.00 2664 98 0.2222 0.2787 REMARK 3 10 3.0014 - 2.8978 1.00 2547 176 0.2136 0.2613 REMARK 3 11 2.8978 - 2.8072 1.00 2600 148 0.2373 0.3094 REMARK 3 12 2.8072 - 2.7270 1.00 2645 129 0.2398 0.2937 REMARK 3 13 2.7270 - 2.6552 1.00 2615 139 0.2684 0.3180 REMARK 3 14 2.6552 - 2.5904 1.00 2581 156 0.2701 0.3534 REMARK 3 15 2.5904 - 2.5315 1.00 2608 156 0.2768 0.3223 REMARK 3 16 2.5315 - 2.4777 1.00 2623 133 0.2650 0.3358 REMARK 3 17 2.4777 - 2.4281 1.00 2597 132 0.2747 0.3134 REMARK 3 18 2.4281 - 2.3823 1.00 2627 104 0.2736 0.2692 REMARK 3 19 2.3823 - 2.3397 1.00 2613 124 0.2885 0.2974 REMARK 3 20 2.3397 - 2.3001 1.00 2606 132 0.3132 0.3211 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 : 0.83 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 40.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.660 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.450 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) : 4.24570 REMARK 3 B22 (A**2) : 4.24570 REMARK 3 B33 (A**2) : -1.90320 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.003 4938 REMARK 3 ANGLE : 0.828 6789 REMARK 3 CHIRALITY : 0.051 745 REMARK 3 PLANARITY : 0.003 796 REMARK 3 DIHEDRAL : 16.706 1911 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 294:424) REMARK 3 ORIGIN FOR THE GROUP (A): 41.8340 -43.6623 -17.7206 REMARK 3 T TENSOR REMARK 3 T11: 0.1328 T22: 0.2093 REMARK 3 T33: 0.6258 T12: -0.2499 REMARK 3 T13: 0.2810 T23: -0.1737 REMARK 3 L TENSOR REMARK 3 L11: 0.7319 L22: 0.3105 REMARK 3 L33: 0.3124 L12: 0.2326 REMARK 3 L13: -0.0370 L23: -0.1581 REMARK 3 S TENSOR REMARK 3 S11: -0.0968 S12: 0.1112 S13: -0.4674 REMARK 3 S21: -0.1751 S22: 0.1031 S23: -0.2820 REMARK 3 S31: 0.1846 S32: -0.0168 S33: 0.2675 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 425:600) REMARK 3 ORIGIN FOR THE GROUP (A): 35.1244 -14.5851 -1.7643 REMARK 3 T TENSOR REMARK 3 T11: 0.2602 T22: 0.1600 REMARK 3 T33: 0.1170 T12: -0.0944 REMARK 3 T13: 0.0398 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 0.6954 L22: 0.5783 REMARK 3 L33: 0.7450 L12: 0.3469 REMARK 3 L13: 0.0301 L23: -0.2901 REMARK 3 S TENSOR REMARK 3 S11: -0.1117 S12: 0.1244 S13: -0.0548 REMARK 3 S21: 0.0992 S22: 0.0057 S23: -0.0395 REMARK 3 S31: -0.3539 S32: -0.1919 S33: 0.0519 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 601:651) REMARK 3 ORIGIN FOR THE GROUP (A): 10.9087 -16.3015 -15.8915 REMARK 3 T TENSOR REMARK 3 T11: 0.3008 T22: 0.6791 REMARK 3 T33: 0.1351 T12: 0.0869 REMARK 3 T13: -0.0094 T23: 0.0758 REMARK 3 L TENSOR REMARK 3 L11: 1.6666 L22: 0.7611 REMARK 3 L33: 1.4417 L12: 0.4427 REMARK 3 L13: 0.0395 L23: -0.2586 REMARK 3 S TENSOR REMARK 3 S11: -0.0705 S12: -0.2359 S13: 0.1597 REMARK 3 S21: -0.0226 S22: 0.1477 S23: 0.1925 REMARK 3 S31: -0.4585 S32: -0.5743 S33: 0.0310 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 652:705) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5795 -16.4818 0.7820 REMARK 3 T TENSOR REMARK 3 T11: 0.5594 T22: 0.9603 REMARK 3 T33: 0.2558 T12: 0.2474 REMARK 3 T13: 0.0473 T23: 0.0553 REMARK 3 L TENSOR REMARK 3 L11: 0.5269 L22: 0.8749 REMARK 3 L33: 1.1122 L12: 0.1569 REMARK 3 L13: 0.0067 L23: 0.6987 REMARK 3 S TENSOR REMARK 3 S11: 0.0765 S12: -0.1714 S13: 0.1160 REMARK 3 S21: 0.2799 S22: 0.1007 S23: 0.0625 REMARK 3 S31: -0.4408 S32: -0.0713 S33: -0.0343 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 706:832) REMARK 3 ORIGIN FOR THE GROUP (A): 20.3441 -26.2529 -15.9052 REMARK 3 T TENSOR REMARK 3 T11: 0.0879 T22: 0.5506 REMARK 3 T33: -0.0201 T12: -0.1847 REMARK 3 T13: 0.0716 T23: 0.0730 REMARK 3 L TENSOR REMARK 3 L11: 0.4347 L22: 0.4363 REMARK 3 L33: 0.5715 L12: 0.2794 REMARK 3 L13: -0.0182 L23: 0.1325 REMARK 3 S TENSOR REMARK 3 S11: -0.1799 S12: 0.1733 S13: -0.0336 REMARK 3 S21: -0.2376 S22: 0.1464 S23: 0.0344 REMARK 3 S31: -0.0413 S32: -0.3480 S33: -0.2884 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B) REMARK 3 ORIGIN FOR THE GROUP (A): 37.1969 -23.4394 4.1306 REMARK 3 T TENSOR REMARK 3 T11: 0.0752 T22: 0.3139 REMARK 3 T33: 0.2562 T12: 0.1479 REMARK 3 T13: -0.1035 T23: 0.0561 REMARK 3 L TENSOR REMARK 3 L11: 0.6235 L22: 0.3332 REMARK 3 L33: 0.4722 L12: -0.0308 REMARK 3 L13: -0.0199 L23: 0.0907 REMARK 3 S TENSOR REMARK 3 S11: 0.0853 S12: 0.1256 S13: -0.1333 REMARK 3 S21: 0.0252 S22: -0.0845 S23: -0.2740 REMARK 3 S31: 0.0456 S32: 0.2078 S33: -0.0135 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN C) REMARK 3 ORIGIN FOR THE GROUP (A): 37.4065 -24.4136 5.4707 REMARK 3 T TENSOR REMARK 3 T11: 0.1659 T22: 0.2669 REMARK 3 T33: 0.2459 T12: 0.1110 REMARK 3 T13: -0.0905 T23: 0.0621 REMARK 3 L TENSOR REMARK 3 L11: 0.4855 L22: 0.5796 REMARK 3 L33: 1.1575 L12: 0.3894 REMARK 3 L13: 0.2679 L23: -0.0327 REMARK 3 S TENSOR REMARK 3 S11: -0.1260 S12: -0.1737 S13: -0.1043 REMARK 3 S21: 0.2281 S22: 0.0848 S23: -0.1806 REMARK 3 S31: 0.0752 S32: 0.0576 S33: -0.0519 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 3RRG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.960 REMARK 200 R MERGE (I) : 0.14600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 9.82 REMARK 200 R MERGE FOR SHELL (I) : 0.91400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.520 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX DEV_704 REMARK 200 STARTING MODEL: PDB ENTRY 3LWL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M NA CACODYLATE PH 6.5, 0.2 M REMARK 280 NH4OAC, 0.01 M MG(OAC)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.32200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.64400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.64400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.32200 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 144 LIES ON A SPECIAL POSITION. 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 ALA A 293 REMARK 465 ALA A 653 REMARK 465 VAL A 654 REMARK 465 ASP A 655 REMARK 465 PRO A 656 REMARK 465 DA C 201 REMARK 465 DA C 202 REMARK 465 DA C 203 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 MET A 646 CG SD CE REMARK 470 PHE A 647 CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL A 649 CG1 CG2 REMARK 470 ARG A 651 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 652 CG CD OE1 OE2 REMARK 470 GLN A 680 CG CD OE1 NE2 REMARK 470 GLU A 681 CG CD OE1 OE2 REMARK 470 GLU A 688 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 B 106 O4' - C1' - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DDG B 112 O3' - P - OP2 ANGL. DEV. = 9.1 DEGREES REMARK 500 DG C 213 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 3.0 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 GLU A 423 66.42 -117.48 REMARK 500 VAL A 433 -63.97 -126.29 REMARK 500 HIS A 526 139.84 -173.89 REMARK 500 TYR A 545 -60.03 -120.83 REMARK 500 VAL A 586 -16.53 -157.87 REMARK 500 PHE A 647 -87.90 -105.22 REMARK 500 PRO A 650 -119.41 -98.88 REMARK 500 ARG A 651 95.58 -51.55 REMARK 500 MET A 658 144.15 73.35 REMARK 500 ARG A 660 15.48 -68.44 REMARK 500 PHE A 700 76.10 -117.15 REMARK 500 HIS A 784 -59.49 72.89 REMARK 500 TYR A 811 95.07 -176.49 REMARK 500 LYS A 831 -152.00 -67.39 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 833 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 4 O REMARK 620 2 HOH A 5 O 107.8 REMARK 620 3 ASP A 372 OD2 118.3 101.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DG3 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 836 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LWL RELATED DB: PDB REMARK 900 RELATED ID: 3RR7 RELATED DB: PDB REMARK 900 RELATED ID: 3RR8 RELATED DB: PDB REMARK 900 RELATED ID: 3RRH RELATED DB: PDB DBREF 3RRG A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3RRG B 101 112 PDB 3RRG 3RRG 101 112 DBREF 3RRG C 201 216 PDB 3RRG 3RRG 201 216 SEQRES 1 A 540 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 2 A 540 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 3 A 540 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 4 A 540 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 5 A 540 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 6 A 540 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 7 A 540 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 8 A 540 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 9 A 540 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 10 A 540 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 11 A 540 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 12 A 540 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 13 A 540 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 540 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 540 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 540 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 540 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 540 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 540 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 20 A 540 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 21 A 540 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 540 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 540 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 540 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 540 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 540 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 540 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 540 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 540 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 540 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 540 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 540 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 540 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 540 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 540 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET SEQRES 36 A 540 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 540 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 540 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 540 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 540 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 540 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 540 ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC DDG SEQRES 1 C 16 DA DA DA 3DR DC DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 3RRG DDG B 112 DG HET DDG B 112 21 HET 3DR C 204 11 HET DG3 A 1 30 HET NA A 833 1 HET GOL A 834 6 HET ACT A 835 4 HET GOL A 836 6 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 3 3DR C5 H11 O6 P FORMUL 4 DG3 C10 H16 N5 O12 P3 FORMUL 5 NA NA 1+ FORMUL 6 GOL 2(C3 H8 O3) FORMUL 7 ACT C2 H3 O2 1- FORMUL 9 HOH *140(H2 O) HELIX 1 1 GLU A 337 ARG A 343 1 7 HELIX 2 2 LEU A 352 GLU A 363 1 12 HELIX 3 3 ASP A 372 ASP A 381 1 10 HELIX 4 4 THR A 386 TYR A 394 1 9 HELIX 5 5 GLU A 401 GLU A 421 1 21 HELIX 6 6 GLU A 423 VAL A 433 1 11 HELIX 7 7 VAL A 433 GLY A 448 1 16 HELIX 8 8 ASP A 452 ALA A 478 1 27 HELIX 9 9 SER A 486 ASP A 496 1 11 HELIX 10 10 SER A 515 LEU A 522 1 8 HELIX 11 11 HIS A 526 TYR A 545 1 20 HELIX 12 12 LEU A 549 ILE A 553 5 5 HELIX 13 13 THR A 588 ARG A 596 1 9 HELIX 14 14 GLN A 613 GLY A 624 1 12 HELIX 15 15 ASP A 625 GLU A 634 1 10 HELIX 16 16 ASP A 637 ALA A 643 1 7 HELIX 17 17 MET A 658 LEU A 670 1 13 HELIX 18 18 SER A 674 LEU A 682 1 9 HELIX 19 19 PRO A 685 ILE A 693 1 9 HELIX 20 20 ILE A 693 PHE A 700 1 8 HELIX 21 21 PHE A 700 GLY A 718 1 19 HELIX 22 22 PRO A 731 ALA A 735 5 5 HELIX 23 23 VAL A 737 MET A 775 1 39 HELIX 24 24 ARG A 795 GLY A 809 1 15 HELIX 25 25 ASP A 826 LYS A 831 1 6 SHEET 1 A 4 GLU A 296 PRO A 298 0 SHEET 2 A 4 VAL A 332 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 A 4 LEU A 321 ALA A 327 -1 N ALA A 326 O HIS A 333 SHEET 4 A 4 PHE A 306 LEU A 311 -1 N VAL A 310 O LEU A 322 SHEET 1 B 2 ARG A 450 LEU A 451 0 SHEET 2 B 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 C 2 ARG A 563 ASN A 565 0 SHEET 2 C 2 SER A 575 SER A 577 -1 O SER A 575 N ASN A 565 SHEET 1 D 4 ARG A 778 GLN A 782 0 SHEET 2 D 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 D 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 D 4 VAL A 819 GLY A 824 -1 O GLY A 824 N LEU A 606 SHEET 1 E 2 TYR A 719 GLU A 721 0 SHEET 2 E 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DDG B 112 1555 1555 1.60 LINK O3' 3DR C 204 P DC C 205 1555 1555 1.61 LINK O HOH A 4 NA NA A 833 1555 1555 3.01 LINK O HOH A 5 NA NA A 833 1555 1555 3.12 LINK OD2 ASP A 372 NA NA A 833 1555 1555 3.10 CISPEP 1 TRP A 299 PRO A 300 0 6.12 CISPEP 2 ASP A 578 PRO A 579 0 1.17 CISPEP 3 GLY A 648 VAL A 649 0 1.05 CISPEP 4 VAL A 649 PRO A 650 0 -6.02 SITE 1 AC1 12 HOH A 123 HOH A 140 HOH A 145 ARG A 587 SITE 2 AC1 12 GLN A 613 HIS A 639 ARG A 659 ARG A 660 SITE 3 AC1 12 LYS A 663 PHE A 667 TYR A 671 DDG B 112 SITE 1 AC2 4 HOH A 4 ALA A 353 LYS A 354 ASP A 372 SITE 1 AC3 3 ARG A 425 TRP A 428 PHE A 724 SITE 1 AC4 2 ARG A 313 LEU A 552 SITE 1 AC5 7 HOH A 134 THR A 544 PRO A 579 ASN A 580 SITE 2 AC5 7 ASN A 583 DC C 209 DC C 210 CRYST1 110.279 110.279 90.966 90.00 90.00 120.00 P 31 2 1 6 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 0.009068 0.005235 0.000000 0.00000 SCALE2 0.000000 0.010471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010993 0.00000