PDB Short entry for 3RR8 HEADER TRANSFERASE/DNA 29-APR-11 3RR8 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: PET-21B; 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 3RR8 1 REMARK LINK REVDAT 3 09-MAY-12 3RR8 1 JRNL REVDAT 2 22-FEB-12 3RR8 1 JRNL REVDAT 1 15-FEB-12 3RR8 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. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_613) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24603 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1274 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 47.1923 - 4.9906 1.00 2717 156 0.1705 0.2036 REMARK 3 2 4.9906 - 3.9618 1.00 2625 136 0.1615 0.2265 REMARK 3 3 3.9618 - 3.4612 1.00 2579 160 0.1883 0.2336 REMARK 3 4 3.4612 - 3.1448 1.00 2573 138 0.2186 0.2863 REMARK 3 5 3.1448 - 2.9194 1.00 2606 128 0.2412 0.2904 REMARK 3 6 2.9194 - 2.7473 1.00 2553 140 0.2400 0.3215 REMARK 3 7 2.7473 - 2.6098 1.00 2577 140 0.2577 0.3145 REMARK 3 8 2.6098 - 2.4962 1.00 2545 152 0.2591 0.3400 REMARK 3 9 2.4962 - 2.4001 1.00 2554 124 0.2624 0.3279 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 : 27.31 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.510 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) : 20.08930 REMARK 3 B22 (A**2) : 20.08930 REMARK 3 B33 (A**2) : 5.35630 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 : 0.002 4925 REMARK 3 ANGLE : 0.681 6769 REMARK 3 CHIRALITY : 0.043 745 REMARK 3 PLANARITY : 0.003 787 REMARK 3 DIHEDRAL : 17.085 1905 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 293:626) REMARK 3 ORIGIN FOR THE GROUP (A): 36.1455 -25.9795 -9.1776 REMARK 3 T TENSOR REMARK 3 T11: -0.0757 T22: -0.0971 REMARK 3 T33: -0.1514 T12: -0.2089 REMARK 3 T13: 0.1232 T23: -0.0515 REMARK 3 L TENSOR REMARK 3 L11: 0.0430 L22: 0.0292 REMARK 3 L33: 0.0174 L12: 0.0612 REMARK 3 L13: -0.0210 L23: -0.0243 REMARK 3 S TENSOR REMARK 3 S11: -0.0539 S12: 0.0656 S13: -0.1862 REMARK 3 S21: 0.0103 S22: 0.0408 S23: -0.0742 REMARK 3 S31: -0.0337 S32: -0.0469 S33: -0.0203 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 627:705) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5405 -15.5529 -3.4188 REMARK 3 T TENSOR REMARK 3 T11: 0.3094 T22: 0.4451 REMARK 3 T33: 0.1245 T12: 0.1791 REMARK 3 T13: 0.0094 T23: 0.0494 REMARK 3 L TENSOR REMARK 3 L11: 0.0120 L22: 0.0029 REMARK 3 L33: 0.0008 L12: 0.0055 REMARK 3 L13: -0.0025 L23: -0.0012 REMARK 3 S TENSOR REMARK 3 S11: 0.0150 S12: -0.0030 S13: 0.0018 REMARK 3 S21: 0.0695 S22: -0.0001 S23: -0.0035 REMARK 3 S31: -0.0320 S32: -0.0383 S33: -0.0080 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 706:832) REMARK 3 ORIGIN FOR THE GROUP (A): 20.0486 -26.1181 -15.5521 REMARK 3 T TENSOR REMARK 3 T11: 0.0538 T22: 0.2341 REMARK 3 T33: -0.0405 T12: -0.1411 REMARK 3 T13: 0.0439 T23: 0.0207 REMARK 3 L TENSOR REMARK 3 L11: 0.0309 L22: 0.0051 REMARK 3 L33: 0.0287 L12: 0.0067 REMARK 3 L13: 0.0315 L23: 0.0071 REMARK 3 S TENSOR REMARK 3 S11: -0.0337 S12: -0.0213 S13: -0.0371 REMARK 3 S21: -0.0293 S22: 0.0179 S23: 0.0228 REMARK 3 S31: -0.0207 S32: -0.0417 S33: -0.0311 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B) REMARK 3 ORIGIN FOR THE GROUP (A): 36.6457 -23.0195 4.1336 REMARK 3 T TENSOR REMARK 3 T11: 0.0180 T22: 0.0918 REMARK 3 T33: 0.0979 T12: 0.0512 REMARK 3 T13: -0.0600 T23: 0.0317 REMARK 3 L TENSOR REMARK 3 L11: 0.0043 L22: 0.0132 REMARK 3 L33: 0.0101 L12: 0.0060 REMARK 3 L13: -0.0036 L23: 0.0019 REMARK 3 S TENSOR REMARK 3 S11: -0.0013 S12: 0.0132 S13: 0.0006 REMARK 3 S21: 0.0037 S22: -0.0037 S23: -0.0024 REMARK 3 S31: -0.0105 S32: -0.0108 S33: -0.0043 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN C) REMARK 3 ORIGIN FOR THE GROUP (A): 35.2117 -24.0420 5.9699 REMARK 3 T TENSOR REMARK 3 T11: 0.0014 T22: 0.0580 REMARK 3 T33: 0.0540 T12: 0.0434 REMARK 3 T13: -0.0713 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.0652 L22: 0.0191 REMARK 3 L33: 0.0072 L12: 0.0213 REMARK 3 L13: 0.0078 L23: 0.0109 REMARK 3 S TENSOR REMARK 3 S11: -0.0249 S12: -0.0013 S13: -0.0104 REMARK 3 S21: 0.0173 S22: -0.0060 S23: -0.0122 REMARK 3 S31: 0.0115 S32: 0.0242 S33: -0.0165 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 3RR8 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_1000065279. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-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) : 1.0007 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) : 2.400 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.540 REMARK 200 R MERGE (I) : 0.14700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.01 REMARK 200 R MERGE FOR SHELL (I) : 0.74700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX DEV_613 REMARK 200 STARTING MODEL: PDB ENTRY 3LWL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 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, 25% 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 30.13533 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 60.27067 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 60.27067 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 30.13533 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: 7340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 83 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 90 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 PRO A 650 REMARK 465 ARG A 651 REMARK 465 GLU A 652 REMARK 465 ALA A 653 REMARK 465 VAL A 654 REMARK 465 ASP A 655 REMARK 465 DA C 201 REMARK 465 DA C 202 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 TRP A 645 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 645 CZ3 CH2 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 PRO A 656 CG CD REMARK 470 LEU A 657 CG CD1 CD2 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 DA C 203 N9 C8 N7 C5 C6 N6 N1 REMARK 480 DA C 203 C2 N3 C4 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DDG B 112 O3' - P - OP2 ANGL. DEV. = 15.1 DEGREES REMARK 500 DDG B 112 O3' - P - OP1 ANGL. DEV. = -17.3 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 294 -83.80 62.39 REMARK 500 ARG A 328 142.54 -171.61 REMARK 500 LEU A 352 38.34 70.26 REMARK 500 THR A 399 -168.76 -106.64 REMARK 500 VAL A 433 -65.87 -135.82 REMARK 500 GLU A 497 32.03 -86.02 REMARK 500 LEU A 498 147.29 -171.81 REMARK 500 HIS A 526 138.53 -179.90 REMARK 500 TYR A 545 -61.92 -122.41 REMARK 500 VAL A 586 -15.36 -161.45 REMARK 500 MET A 646 -75.72 -132.03 REMARK 500 PHE A 647 131.21 -171.46 REMARK 500 LEU A 657 -76.78 169.62 REMARK 500 ARG A 659 163.97 -45.08 REMARK 500 ARG A 660 -21.75 81.85 REMARK 500 ALA A 683 61.56 62.22 REMARK 500 ASP A 732 6.38 -68.45 REMARK 500 LEU A 780 -61.52 -101.39 REMARK 500 HIS A 784 -61.03 76.34 REMARK 500 TYR A 811 107.81 -167.83 REMARK 500 ALA A 814 16.93 -68.47 REMARK 500 REMARK 500 REMARK: NULL 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 GOL 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 GOL A 835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1 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: 3RRG RELATED DB: PDB REMARK 900 RELATED ID: 3RRH RELATED DB: PDB DBREF 3RR8 A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3RR8 B 101 112 PDB 3RR8 3RR8 101 112 DBREF 3RR8 C 201 216 PDB 3RR8 3RR8 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 3RR8 DDG B 112 DG HET DDG B 112 21 HET 3DR C 204 11 HET DG3 A 1 30 HET GOL A 833 6 HET GOL A 834 6 HET GOL A 835 6 HET GOL B 1 6 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL 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 GOL 4(C3 H8 O3) FORMUL 9 HOH *101(H2 O) HELIX 1 1 GLU A 337 LEU A 342 1 6 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 LEU A 420 1 20 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 GLY A 479 1 28 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 THR A 642 1 6 HELIX 17 17 ARG A 660 LEU A 670 1 11 HELIX 18 18 SER A 674 ALA A 683 1 10 HELIX 19 19 TYR A 686 PHE A 700 1 15 HELIX 20 20 PHE A 700 GLY A 718 1 19 HELIX 21 21 PRO A 731 ALA A 735 5 5 HELIX 22 22 VAL A 737 GLU A 774 1 38 HELIX 23 23 LYS A 793 GLY A 809 1 17 SHEET 1 A 3 PHE A 306 LEU A 311 0 SHEET 2 A 3 LEU A 321 ALA A 327 -1 O ALA A 327 N PHE A 306 SHEET 3 A 3 VAL A 332 ARG A 334 -1 O HIS A 333 N ALA A 326 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' DA C 203 P 3DR C 204 1555 1555 1.61 LINK O3' 3DR C 204 P DC C 205 1555 1555 1.61 CISPEP 1 TRP A 299 PRO A 300 0 3.86 CISPEP 2 ASP A 578 PRO A 579 0 -2.64 CISPEP 3 GLY A 648 VAL A 649 0 0.29 SITE 1 AC1 8 ARG A 587 GLN A 613 HIS A 639 ARG A 659 SITE 2 AC1 8 LYS A 663 PHE A 667 TYR A 671 DDG B 112 SITE 1 AC2 7 HOH A 53 THR A 544 TYR A 545 PRO A 579 SITE 2 AC2 7 ASN A 580 DC C 209 DC C 210 SITE 1 AC3 4 ARG A 313 TRP A 318 LEU A 552 DC C 216 SITE 1 AC4 2 TRP A 428 PHE A 724 SITE 1 AC5 4 HOH B 8 DC B 106 DG B 107 DC C 209 CRYST1 108.965 108.965 90.406 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 0.009177 0.005298 0.000000 0.00000 SCALE2 0.000000 0.010597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011061 0.00000