HEADER TRANSFERASE/DNA 24-FEB-10 3LWL TITLE STRUCTURE OF KLENOW FRAGMENT OF TAQ POLYMERASE IN COMPLEX WITH AN TITLE 2 ABASIC SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KLENOW FRAGMENT, UNP RESIDUES 293-832; 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: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA PRIMER; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*AP*AP*(3DR) COMPND 15 P*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: DNA TEMPLATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POL1, POLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC DNA; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: SYNTHETIC DNA KEYWDS DNA REPLICATION, DNA REPAIR, DNA POLYMERASES, ABASIC SITES, KEYWDS 2 TRANSLESION SYNTHESIS, DNA DAMAGE, DNA-BINDING, DNA-DIRECTED DNA KEYWDS 3 POLYMERASE, AMINO ACID-TEMPLATING MECHANISM, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,S.OBEID REVDAT 3 01-NOV-23 3LWL 1 REMARK LINK REVDAT 2 12-FEB-14 3LWL 1 JRNL VERSN REVDAT 1 05-MAY-10 3LWL 0 JRNL AUTH S.OBEID,N.BLATTER,R.KRANASTER,A.SCHNUR,K.DIEDERICHS,W.WELTE, JRNL AUTH 2 A.MARX JRNL TITL REPLICATION THROUGH AN ABASIC DNA LESION: STRUCTURAL BASIS JRNL TITL 2 FOR ADENINE SELECTIVITY JRNL REF EMBO J. V. 29 1738 2010 JRNL REFN ISSN 0261-4189 JRNL PMID 20400942 JRNL DOI 10.1038/EMBOJ.2010.64 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30730 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1560 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 47.7408 - 5.0026 1.00 2784 160 0.1685 0.2130 REMARK 3 2 5.0026 - 3.9713 1.00 2685 141 0.1490 0.1806 REMARK 3 3 3.9713 - 3.4695 1.00 2653 153 0.1570 0.1900 REMARK 3 4 3.4695 - 3.1523 1.00 2643 150 0.1895 0.2361 REMARK 3 5 3.1523 - 2.9264 1.00 2669 136 0.2016 0.2813 REMARK 3 6 2.9264 - 2.7539 1.00 2624 139 0.2177 0.2654 REMARK 3 7 2.7539 - 2.6160 1.00 2626 149 0.2224 0.2837 REMARK 3 8 2.6160 - 2.5021 1.00 2620 147 0.2276 0.2766 REMARK 3 9 2.5021 - 2.4058 1.00 2623 127 0.2290 0.2709 REMARK 3 10 2.4058 - 2.3228 1.00 2665 121 0.2311 0.2711 REMARK 3 11 2.3228 - 2.2502 0.99 2578 137 0.2499 0.2834 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 : 0.35 REMARK 3 B_SOL : 42.92 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.46700 REMARK 3 B22 (A**2) : -0.46700 REMARK 3 B33 (A**2) : 0.93300 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 : 0.016 4992 REMARK 3 ANGLE : 0.929 6841 REMARK 3 CHIRALITY : 0.056 745 REMARK 3 PLANARITY : 0.003 797 REMARK 3 DIHEDRAL : 18.469 1913 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 295:627) REMARK 3 ORIGIN FOR THE GROUP (A): 36.1207 -26.1347 -9.2346 REMARK 3 T TENSOR REMARK 3 T11: 0.0785 T22: 0.1502 REMARK 3 T33: 0.1484 T12: -0.0757 REMARK 3 T13: 0.0498 T23: -0.0314 REMARK 3 L TENSOR REMARK 3 L11: 1.7432 L22: 1.0079 REMARK 3 L33: 1.6840 L12: 1.0417 REMARK 3 L13: -0.2018 L23: -0.4845 REMARK 3 S TENSOR REMARK 3 S11: -0.1668 S12: 0.2947 S13: -0.3503 REMARK 3 S21: -0.0840 S22: 0.1199 S23: -0.3073 REMARK 3 S31: -0.2679 S32: -0.2174 S33: 0.0019 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 628:697) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4281 -14.0125 -3.3679 REMARK 3 T TENSOR REMARK 3 T11: 0.7355 T22: 1.1348 REMARK 3 T33: 0.2708 T12: 0.5210 REMARK 3 T13: 0.0428 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 5.8724 L22: 4.3514 REMARK 3 L33: 0.1501 L12: -1.6437 REMARK 3 L13: 0.5349 L23: -0.7910 REMARK 3 S TENSOR REMARK 3 S11: -0.0849 S12: -0.3173 S13: 0.2347 REMARK 3 S21: 0.9439 S22: 0.6137 S23: 0.1279 REMARK 3 S31: -1.0082 S32: -0.7969 S33: -0.3477 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 698:832) REMARK 3 ORIGIN FOR THE GROUP (A): 18.9929 -26.2947 -15.0833 REMARK 3 T TENSOR REMARK 3 T11: 0.1238 T22: 0.5629 REMARK 3 T33: 0.0105 T12: -0.0867 REMARK 3 T13: 0.0327 T23: 0.0372 REMARK 3 L TENSOR REMARK 3 L11: 1.0174 L22: 0.7696 REMARK 3 L33: 2.4774 L12: 0.3704 REMARK 3 L13: 0.3617 L23: 0.0507 REMARK 3 S TENSOR REMARK 3 S11: -0.3414 S12: 0.4929 S13: -0.0986 REMARK 3 S21: -0.2824 S22: 0.4156 S23: -0.0808 REMARK 3 S31: -0.1770 S32: -1.0274 S33: -0.1632 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 101:112) REMARK 3 ORIGIN FOR THE GROUP (A): 37.3551 -23.5219 4.2489 REMARK 3 T TENSOR REMARK 3 T11: 0.0915 T22: 0.2617 REMARK 3 T33: 0.1725 T12: 0.0380 REMARK 3 T13: -0.0063 T23: 0.0596 REMARK 3 L TENSOR REMARK 3 L11: 1.3556 L22: 2.7281 REMARK 3 L33: 4.7691 L12: 0.4448 REMARK 3 L13: 0.5419 L23: -2.6211 REMARK 3 S TENSOR REMARK 3 S11: -0.1011 S12: 0.3964 S13: -0.1064 REMARK 3 S21: 0.2560 S22: -0.3546 S23: -0.4148 REMARK 3 S31: -0.3786 S32: 0.2923 S33: 0.4291 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN C AND RESID 203:216) REMARK 3 ORIGIN FOR THE GROUP (A): 35.6396 -24.4744 5.9074 REMARK 3 T TENSOR REMARK 3 T11: 0.1573 T22: 0.2186 REMARK 3 T33: 0.1950 T12: 0.0572 REMARK 3 T13: -0.0687 T23: 0.0641 REMARK 3 L TENSOR REMARK 3 L11: 1.1021 L22: 0.8395 REMARK 3 L33: 1.6975 L12: 0.8486 REMARK 3 L13: -1.0360 L23: -0.4118 REMARK 3 S TENSOR REMARK 3 S11: -0.2737 S12: 0.0592 S13: -0.3157 REMARK 3 S21: 0.1248 S22: 0.1936 S23: -0.2142 REMARK 3 S31: 0.0190 S32: -0.0237 S33: 0.0275 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 3LWL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000057820. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS (DCCM) IN (+ REMARK 200 --+) GEOMETRY, AND A TOROIDAL REMARK 200 MIRROR (M2) REMARK 200 OPTICS : VERTICALLY COLLIMATING MIRROR REMARK 200 (M1, FOCUS AT INFINITY), REMARK 200 FOLLOWED BY A BARTELS REMARK 200 MONOCHROMATOR WITH DUAL CHANNEL REMARK 200 CUT CRYSTALS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30775 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.78 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 9.94 REMARK 200 R MERGE FOR SHELL (I) : 0.97100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.480 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.6_289 REMARK 200 STARTING MODEL: PDB ENTRY 3KTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M SODIUM CACODYLATE, 0.2M AMMONIUM REMARK 280 ACETATE, 0.01M MAGNESIUM ACETATE, 30% PEG 8000, PH 7, VAPOR REMARK 280 DIFFUSION, HANGING 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 30.42167 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 60.84333 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 60.84333 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 30.42167 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: 6430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 C ACT A 2 LIES ON A SPECIAL POSITION. REMARK 375 O ACT A 2 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 LEU A 294 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 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 THR A 642 OG1 CG2 REMARK 470 SER A 644 OG 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2B DDS A 1 O HOH A 846 2.00 REMARK 500 O HOH A 845 O HOH A 846 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 103 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 203 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 213 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 214 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DG C 214 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 2.4 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 THR A 399 -165.02 -108.60 REMARK 500 VAL A 433 -70.26 -129.90 REMARK 500 HIS A 526 135.60 -174.98 REMARK 500 TYR A 545 -59.40 -120.46 REMARK 500 VAL A 586 -19.07 -161.18 REMARK 500 PHE A 647 153.82 -29.18 REMARK 500 LEU A 682 -1.78 -146.73 REMARK 500 ASP A 732 3.40 -69.04 REMARK 500 HIS A 784 -56.70 72.20 REMARK 500 TYR A 811 94.82 -172.52 REMARK 500 LYS A 831 51.66 -91.42 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 MG A 833 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DDS A 1 O3G REMARK 620 2 DDS A 1 O2B 56.6 REMARK 620 3 DDS A 1 O2A 64.6 61.1 REMARK 620 4 HOH A 845 O 106.4 49.9 77.7 REMARK 620 5 HOH A 846 O 83.8 48.8 109.1 52.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDS A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 833 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 834 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 835 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 836 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 837 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 838 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 839 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KTQ RELATED DB: PDB REMARK 900 RELATED ID: 3LWM RELATED DB: PDB DBREF 3LWL A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 3LWL B 101 112 PDB 3LWL 3LWL 101 112 DBREF 3LWL C 201 216 PDB 3LWL 3LWL 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 2DA SEQRES 1 C 16 DA DA DA 3DR DT DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC MODRES 3LWL 2DA B 112 DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HET 2DA B 112 20 HET 3DR C 204 11 HET DDS A 1 29 HET MG A 833 1 HET ACT A 2 4 HET ACT A 3 4 HET ACT A 5 4 HET GOL A 834 6 HET GOL A 835 6 HET GOL A 836 6 HET GOL A 6 6 HET GOL A 7 6 HET NA A 837 1 HET NA A 838 1 HET NA A 839 1 HET NA A 4 1 HET GOL B 4 6 HET GOL B 8 6 HET ACT C 1 4 HET ACT C 6 4 HETNAM 2DA 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM DDS 2',3'-DIDEOXYADENOSINE TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 2DA C10 H14 N5 O5 P FORMUL 3 3DR C5 H11 O6 P FORMUL 4 DDS C10 H16 N5 O11 P3 FORMUL 5 MG MG 2+ FORMUL 6 ACT 5(C2 H3 O2 1-) FORMUL 9 GOL 7(C3 H8 O3) FORMUL 14 NA 4(NA 1+) FORMUL 22 HOH *161(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 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 ALA A 521 1 7 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 SER A 644 MET A 646 5 3 HELIX 18 18 MET A 658 GLY A 672 1 15 HELIX 19 19 SER A 674 GLU A 681 1 8 HELIX 20 20 PRO A 685 PHE A 700 1 16 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 GLY A 776 1 40 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 ALA A 297 0 SHEET 2 A 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 A 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 A 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 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 577 N ARG A 563 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 2DA B 112 1555 1555 1.61 LINK O3' DA C 203 P 3DR C 204 1555 1555 1.60 LINK O3' 3DR C 204 P DT C 205 1555 1555 1.59 LINK O3G DDS A 1 MG MG A 833 1555 1555 2.58 LINK O2B DDS A 1 MG MG A 833 1555 1555 2.66 LINK O2A DDS A 1 MG MG A 833 1555 1555 2.74 LINK MG MG A 833 O HOH A 845 1555 1555 2.76 LINK MG MG A 833 O HOH A 846 1555 1555 1.84 CISPEP 1 TRP A 299 PRO A 300 0 4.78 CISPEP 2 ASP A 578 PRO A 579 0 3.76 SITE 1 AC1 11 ARG A 587 GLN A 613 HIS A 639 ARG A 659 SITE 2 AC1 11 LYS A 663 PHE A 667 TYR A 671 MG A 833 SITE 3 AC1 11 HOH A 845 HOH A 846 2DA B 112 SITE 1 AC2 4 DDS A 1 GLU A 820 HOH A 845 HOH A 846 SITE 1 AC3 2 ARG A 313 LEU A 552 SITE 1 AC4 4 LYS A 542 SER A 543 ASP A 547 HOH C 92 SITE 1 AC5 8 THR A 544 TYR A 545 PRO A 579 ASN A 580 SITE 2 AC5 8 ASN A 583 HOH C 7 DC C 209 DC C 210 SITE 1 AC6 3 ARG A 425 TRP A 428 PHE A 724 SITE 1 AC7 10 HOH A 53 HOH A 69 HOH A 100 HOH A 126 SITE 2 AC7 10 LYS A 354 ASP A 355 ARG A 563 PHE A 564 SITE 3 AC7 10 ASN A 565 GLN A 566 SITE 1 AC8 8 GLU A 315 PRO A 316 MET A 317 GLU A 445 SITE 2 AC8 8 HIS A 561 THR A 562 ARG A 563 ASP A 578 SITE 1 AC9 2 VAL A 737 SER A 739 SITE 1 BC1 5 PRO A 316 LYS A 354 ASP A 355 GLU A 445 SITE 2 BC1 5 ARG A 563 SITE 1 BC2 3 LYS A 314 ASP A 578 DC C 209 SITE 1 BC3 2 ASP A 381 SER A 383 SITE 1 BC4 2 ALA A 568 DC C 207 SITE 1 BC5 8 HOH B 35 HOH B 55 DC B 106 DG B 107 SITE 2 BC5 8 DG B 108 HOH B 113 HOH B 161 DC C 209 SITE 1 BC6 8 HOH A 123 LYS A 540 DG B 107 DG B 108 SITE 2 BC6 8 DC B 109 HOH B 155 ACT C 6 HOH C 81 SITE 1 BC7 3 ARG A 728 DG C 206 DC C 207 SITE 1 BC8 9 ASN A 485 SER A 486 ARG A 487 GOL B 8 SITE 2 BC8 9 HOH B 60 HOH B 119 HOH C 128 DG C 211 SITE 3 BC8 9 DT C 212 CRYST1 110.228 110.228 91.265 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 0.009072 0.005238 0.000000 0.00000 SCALE2 0.000000 0.010476 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010957 0.00000